R Notebook

library("tidyverse")
library("data.table")
library("rtracklayer")
library("ggrastr")
library("glue")
library("DESeq2")
library("ggpubr")
library("wigglescout")
library("eulerr")
library("ggplot2")
library(corrplot)
library(bedscout)

# export 
result_folder = "../results/"
plot_folder = "../results/plots/"
stat_output = "../results/stats/"

combined_bigwigs <- list.files("../mendeley/Figure2","CTCF_ChIP-seq.+bw",
                  full.names = TRUE)
geo_bigwigs <- list.files("../mendeley/Figure2","GSM.+bw",
                  full.names = TRUE)
geo_CnR_bigwigs <- list.files("../mendeley/FigureS2","GSM.+bw",
                  full.names = TRUE)

# colors
mypal <-c("cornflowerblue","orange","red2","darkgreen","#505050")
mypal <-c("#00619D","#A82A34","orange","seagreen","#505050")
mypal2 <-c("#00619D","#7FB0CE","#A82A34","#D39499","orange","#FFD55A","seagreen","#7DBA9C","#505050")

# diff signal function
bw_granges_diff_analysis <- function(granges_c1,
                                     granges_c2,
                                     label_c1,
                                     label_c2,
                                     estimate_size_factors = FALSE,
                                     as_granges = FALSE) {
  # Bind first, get numbers after
  names_values <- NULL
  fields <- names(mcols(granges_c1))
  
  if ("name" %in% fields) {
    names_values <- mcols(granges_c1)[["name"]]
    granges_c1 <- granges_c1[, fields[fields != "name"]]
  }
  
  fields <- names(mcols(granges_c2))
  if ("name" %in% fields) {
    granges_c2 <- granges_c2[, fields[fields != "name"]]
  }
  
  cts_df <- cbind(data.frame(granges_c1), mcols(granges_c2))
  
  if (!is.null(names_values)) {
    rownames(cts_df) <- names_values
  }
  
  # Needs to drop non-complete cases and match rows
  complete <- complete.cases(cts_df)
  cts_df <- cts_df[complete, ]
  
  values_df <- cts_df[, 6:ncol(cts_df)] %>% dplyr::select(where(is.numeric))
  cts <- get_nreads_columns(values_df)
  
  condition_labels <- c(rep(label_c1, length(mcols(granges_c1))), rep(label_c2, length(mcols(granges_c2))))
  
  
  coldata <- data.frame(colnames(cts), condition = as.factor(condition_labels))
  print(coldata)
  
  dds <- DESeq2::DESeqDataSetFromMatrix(
    countData = cts,
    colData = coldata,
    design = ~ condition,
    rowRanges = granges_c1[complete, ]
  )
  
  
  if (estimate_size_factors == TRUE) {
    dds <- DESeq2::estimateSizeFactors(dds)
  }
  else {
    # Since files are scaled, we do not want to estimate size factors
    sizeFactors(dds) <- c(rep(1, ncol(cts)))
  }
  
  dds <- DESeq2::estimateDispersions(dds)
  dds <- DESeq2::nbinomWaldTest(dds)
  
  if (as_granges) {
    result <- DESeq2::results(dds, format = "GRanges", alpha = 0.01)
    if (!is.null(names_values)) {
      result$name <- names_values[complete]
    }
    
  }
  else {
    # result <- results(dds, format="DataFrame")
    result <- dds
  }
  
  result
}

get_nreads_columns <- function(df, length_factor = 100) {
  # Convert mean coverages to round integer read numbers
  cts <- as.matrix(df)
  cts <- as.matrix(cts[complete.cases(cts), ])
  cts <- round(cts * length_factor)
  cts
}

ctcf.and.G4.pro <- import("../peaks/G4 CTCF_with_promoters_sorted.bed")
ctcf.not.G4.pro <- import("../peaks/CTCF-only_with_promoters_sorted.bed")
ctcf.and.G4.npr <- import("../peaks/G4 CTCF_without_promoters_sorted.bed")
ctcf.not.G4.npr <- import("../peaks/CTCF-only_without_promoters_sorted.bed")

ctcf.and.G4.pro$class <- "CTCF_and_G4"
ctcf.not.G4.pro$class <- "CTCF_not_G4"
ctcf.and.G4.npr$class <- "CTCF_and_G4"
ctcf.not.G4.npr$class <- "CTCF_not_G4"
ctcf.and.G4.pro$pro <- "Pro"
ctcf.not.G4.pro$pro <- "Pro"
ctcf.and.G4.npr$pro <- "noPro"
ctcf.not.G4.npr$pro <- "noPro"

ctcf.and.G4 <- c(ctcf.and.G4.pro,ctcf.and.G4.npr)
ctcf.not.G4 <- c(ctcf.not.G4.pro,ctcf.not.G4.npr)
ctcf <- c(ctcf.and.G4,ctcf.not.G4)
ctcf <- sortSeqlevels(ctcf)
ctcf <- sort(ctcf)
names(ctcf) <- paste0(ctcf$class," ",ctcf$pro)
peaks_bed <- "../peaks/CTCF_G4_in_6_categories.bed"
export.bed(ctcf, peaks_bed)

check MACS peak widths

ctcf.raw <- import("../peaks/CTCF_mES_peaks.narrowPeak")
G4.raw <- import("../peaks/G4_WT_peaks.narrowPeak")
ctcf.raw$class <- "CTCF"
G4.raw$class <- "G4"
ctcf.raw$pro <- "NA"
G4.raw$pro <- "NA"
df <- rbind(as.data.frame(ctcf.raw)[c(1,2,3,4,5,12,13)], as.data.frame(G4.raw)[c(1,2,3,4,5,12,13)],as.data.frame(ctcf,row.names = NULL))
ggdensity(df,x="width",y = "density",color = "class", fill="class", alpha=0.1, palette=mypal) + scale_x_continuous(limits = c(100,600))

Warning: Removed 3661 rows containing non-finite outside the scale range (`stat_density()`).

min(width(G4.raw))

[1] 233

min(width(ctcf.raw))

[1] 200

median(width(G4.raw))

[1] 316

median(width(ctcf.raw))

[1] 332

calculate coverage over peaks

# Wulfridge CTCF ChIP-Seq mocks
mocks_bigwigs = c("../data/CutNTag_ChIP-Seq/bw/SRR23958387_GSM7116277_E14_Mock_CTCF_Rep1_Mus_musculus_ChIP-Seq.CPMnorm.bw",
          "../data/CutNTag_ChIP-Seq/bw/SRR23958386_GSM7116278_E14_Mock_CTCF_Rep2_Mus_musculus_ChIP-Seq.CPMnorm.bw")

# PDS
# Wulfridge CTCF ChIP-Seq
pds_bigwigs = c("../data/CutNTag_ChIP-Seq/bw/SRR23958385_GSM7116279_E14_PDS_CTCF_Rep1_Mus_musculus_ChIP-Seq.CPMnorm.bw",
                "../data/CutNTag_ChIP-Seq/bw/SRR23958384_GSM7116280_E14_PDS_CTCF_Rep2_Mus_musculus_ChIP-Seq.CPMnorm.bw")

pdc_bigwigs = c("../data/CutNTag_ChIP-Seq/bw/SRR23958383_GSM7116281_E14_PhenDC3_CTCF_Rep1_Mus_musculus_ChIP-Seq.CPMnorm.bw",
                "../data/CutNTag_ChIP-Seq/bw/SRR23958382_GSM7116282_E14_PhenDC3_CTCF_Rep2_Mus_musculus_ChIP-Seq.CPMnorm.bw")

G4_bigwigs = c("../mendeley/Figure1/G4_CUT-Tag_thisStudy.bw")

cov.mocks <- bw_loci(mocks_bigwigs,peaks_bed,labels=c("mock_1","mock_2"))
cov.pds <- bw_loci(pds_bigwigs,peaks_bed,labels=c("PDS_1","PDS_2"))
cov.pdc <- bw_loci(pdc_bigwigs,peaks_bed,labels=c("PhenDC3_1","PhenDC3_2"))
cov.G4 <- bw_loci(G4_bigwigs,peaks_bed,labels=c("G4_NT"))
cov.combined <- bw_loci(combined_bigwigs,peaks_bed,labels=c("mock","PDS","PhenDC3"))
cov.geo <- bw_loci(geo_bigwigs,peaks_bed,labels=c("GEO_mock","GEO_PDS","GEO_PhenDC3"))

quick comparison on deposited and reprocessed bigwig files

corr_df <- data.frame(data.frame(cov.combined)[,c(9,6,7,8)],data.frame(cov.geo)[,6:8],data.frame(cov.mocks)[,6:7],data.frame(cov.pds)[,6:7],data.frame(cov.pdc)[,6:7])
res <- cor(corr_df[,2:13])
corrplot(res, type = "upper", order = "hclust",tl.col = "black", tl.srt = 45,addCoef.col = 'black',tl.pos = 'd',    cl.pos = 'n', col.lim=c(0.93, 1),is.corr = F, method = 'color')

p1 <- plot_bw_profile(c(mocks_bigwigs[1],pds_bigwigs[1],pdc_bigwigs[1]),loci = "../peaks/G4 CTCF_with_promoters_sorted.bed",mode = "center",verbose = F) + coord_cartesian(ylim=c(0,2.4))
p2 <- plot_bw_profile(c(mocks_bigwigs[2],pds_bigwigs[2],pdc_bigwigs[2]),loci = "../peaks/G4 CTCF_with_promoters_sorted.bed",mode = "center",verbose = F) + coord_cartesian(ylim=c(0,2.4))
p3 <- plot_bw_profile(bwfiles = combined_bigwigs,loci = "../peaks/G4 CTCF_with_promoters_sorted.bed",mode = "center",verbose = F) + coord_cartesian(ylim=c(0,2.4))
ggarrange(p1,p2,p3, ncol=3)

p1 <- plot_bw_profile(bwfiles = geo_bigwigs,loci = "../peaks/G4 CTCF_with_promoters_sorted.bed",mode = "center",verbose = F) + coord_cartesian(ylim=c(0,5))
p2 <- plot_bw_profile(bwfiles = combined_bigwigs,loci = "../peaks/G4 CTCF_with_promoters_sorted.bed",mode = "center",verbose = F) + coord_cartesian(ylim=c(0,2.6))
ggarrange(p1,p2, ncol=2)

p1 <- plot_bw_profile(bwfiles = geo_bigwigs,loci = "../peaks/CTCF-only_with_promoters_sorted.bed",mode = "center",verbose = F) + coord_cartesian(ylim=c(0,5))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0538563829787234 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0538563829787234 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0538563829787234 per locus)

p2 <- plot_bw_profile(bwfiles = combined_bigwigs,loci = "../peaks/CTCF-only_with_promoters_sorted.bed",mode = "center",verbose = F) + coord_cartesian(ylim=c(0,2.6))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0538563829787234 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0538563829787234 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0538563829787234 per locus)

ggarrange(p1,p2, ncol=2)

p1 <- plot_bw_loci_scatter(mocks_bigwigs[1],mocks_bigwigs[2], loci = "../peaks/G4 CTCF_with_promoters_sorted.bed", verbose = F)
p2 <- plot_bw_loci_scatter(pds_bigwigs[1],pds_bigwigs[2], loci = "../peaks/G4 CTCF_with_promoters_sorted.bed", verbose = F)
p3 <- plot_bw_loci_scatter(pdc_bigwigs[1],pdc_bigwigs[2], loci = "../peaks/G4 CTCF_with_promoters_sorted.bed", verbose = F)
ggarrange(p1,p2,p3, ncol=3)

p1 <- plot_bw_loci_scatter(combined_bigwigs[1],combined_bigwigs[2], loci = "../peaks/G4 CTCF_with_promoters_sorted.bed", verbose = F)
p2 <- plot_bw_loci_scatter(combined_bigwigs[2],combined_bigwigs[3], loci = "../peaks/G4 CTCF_with_promoters_sorted.bed", verbose = F)
p3 <- plot_bw_loci_scatter(combined_bigwigs[1],combined_bigwigs[3], loci = "../peaks/G4 CTCF_with_promoters_sorted.bed", verbose = F)
ggarrange(p1,p2,p3, ncol=3)

results <- data.frame(
  as.data.frame(cov.mocks),
  as.data.frame(cov.pds)[6:7],
  as.data.frame(cov.pdc)[6:7],
  as.data.frame(cov.G4)[6],
  raw.lfc.pds_1 = log2(cov.pds$PDS_1 / cov.mocks$mock_1),
  raw.lfc.pds_2 = log2(cov.pds$PDS_2 / cov.mocks$mock_2),
  raw.lfc.pdc_1 = log2(cov.pds$PDS_1 / cov.mocks$mock_1),
  raw.lfc.pdc_2 = log2(cov.pdc$PhenDC3_2 / cov.mocks$mock_2),
  raw.lfc.pds = log2(rowMeans(as.data.frame(cov.pds)[6:7]) / rowMeans(as.data.frame(cov.mocks)[6:7])),
  raw.lfc.pdc = log2(rowMeans(as.data.frame(cov.pdc)[6:7]) / rowMeans(as.data.frame(cov.mocks)[6:7])),
  mean.mock = rowMeans(as.data.frame(cov.mocks)[6:7]),
  mean.pds = rowMeans(as.data.frame(cov.pds)[6:7]),
  mean.pdc = rowMeans(as.data.frame(cov.pdc)[6:7])
)

cov.mocks$name <- NULL
cov.pds$name <- NULL
cov.pdc$name <- NULL

de_pds <- bw_granges_diff_analysis(cov.mocks, cov.pds, "Mock", "PDS")

converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

lfc_pds = DESeq2::lfcShrink(de_pds, coef = "condition_PDS_vs_Mock", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

de_pdc <- bw_granges_diff_analysis(cov.mocks, cov.pdc, "Mock", "PhenDC3")

converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

lfc_pdc = DESeq2::lfcShrink(de_pdc, coef = "condition_PhenDC3_vs_Mock", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

results$deseq.lfc.pds <- results(de_pds)$log2FoldChange
results$deseq.lfcs.pds <- lfc_pds$log2FoldChange
results$deseq.padj.pds <- lfc_pds$padj
results$deseq.mean.pds <- log2(lfc_pds$baseMean)
results$deseq.sig.pds <- lfc_pds$pvalue < 0.05

results$deseq.lfc.pdc <- results(de_pdc)$log2FoldChange
results$deseq.lfcs.pdc <- lfc_pdc$log2FoldChange
results$deseq.padj.pdc <- lfc_pdc$padj
results$deseq.mean.pdc <- log2(lfc_pdc$baseMean)
results$deseq.sig.pdc <- lfc_pdc$pvalue < 0.05

results$class <- gsub(" .+", "", results$name)
results$pro <- gsub(".+ ", "", results$name)
results$pro <- factor(results$pro, levels = c("Pro", "noPro"))
results$class <- factor(results$class, levels = c("CTCF_and_G4", "CTCF_not_G4"))

results$log2.mock <- log2(results$mean.mock)
results$log2.pds <- log2(results$mean.pds)
results$log2.pdc <- log2(results$mean.pdc)
results$log2.G4 <- log2(results$G4_NT)

results$deseq.sigup.pds <- results$deseq.sig.pds &
  results$deseq.lfc.pds > 0
results$deseq.sigup.pdc <- results$deseq.sig.pdc &
  results$deseq.lfc.pdc > 0

write.table(results, glue("{result_folder}foldchange_results.txt"))
table(results$name)

CTCF_and_G4 noPro   CTCF_and_G4 Pro CTCF_not_G4 noPro   CTCF_not_G4 Pro 
              988              1300             43309              6016 

#results <- read.table("foldchange_results.txt")
results$class <- factor(results$class, levels = c("CTCF_and_G4", "CTCF_not_G4"))

p <- ggviolin(
  results,
  x = "class",
  y = "mean.mock",
  fill = "class",
  palette = mypal,
  add = "median_iqr"
) + coord_cartesian(ylim = c(0, 10))
annotate_figure(p, fig.lab = "CTCF signal by class in mock condition, mean of two reps, median+iqr", fig.lab.size = 6)

ggsave(glue("{plot_folder}Violin_CTCF_classes.pdf"), last_plot())

Saving 3 x 3 in image

p <- ggviolin(
  results,
  x = "class",
  y = "mean.mock",
  fill = "pro",
  palette = mypal,
  add = "median_iqr"
) + coord_cartesian(ylim = c(0, 10))
annotate_figure(p, fig.lab = "CTCF signal by class in mock condition, mean of two reps, median+iqr", fig.lab.size = 6)

ggsave(glue("{plot_folder}Violin_CTCF_classes_pro.pdf"),
       last_plot())

Saving 3 x 3 in image

mdf <- reshape2::melt(dplyr::select(
  results,
  c(
    "class",
    "mock_1",
    "mock_2",
    "PDS_1",
    "PDS_2",
    "PhenDC3_1",
    "PhenDC3_2"
  )
))

Using class as id variables

ggboxplot(
  mdf,
  x = "variable",
  y = "value",
  fill = "class",
  palette = mypal
) + coord_cartesian(ylim = c(0, 10))

ggsave(glue("{plot_folder}Boxplot_CTCF_reps.pdf"), last_plot())

Saving 5 x 3 in image

mdf <- reshape2::melt(dplyr::select(
  results,
  c(
    "class",
    "mock_1",
    "mock_2",
    "PDS_1",
    "PDS_2",
    "PhenDC3_1",
    "PhenDC3_2"
  )
))

Using class as id variables

mdf_stats_class = compare_means(value ~ class, group.by = "variable", data = mdf)

ggviolin(
  mdf,
  x = "variable",
  y = "value",
  fill = "class",
  palette = mypal,
  add = "median_iqr"
) + coord_cartesian(ylim = c(0, 10))

ggsave(glue("{plot_folder}Violin_CTCF_reps.pdf"), last_plot())

Saving 5 x 3 in image

mdf <- reshape2::melt(dplyr::select(results, c(
  "class", "deseq.lfc.pds", "deseq.lfc.pdc"
)))

Using class as id variables

p <- ggviolin(
  mdf,
  x = "variable",
  y = "value",
  fill = "class",
  palette = mypal,
  add = "median_iqr"
) + geom_hline(yintercept = 0, linetype = "dotted") + coord_cartesian(ylim =
                                                                        c(-3, 3)) + stat_compare_means(aes(group = class), label.y = 3, size = 2)

annotate_figure(p, fig.lab = "DESEq foldchange mean treat vs mean mock, median+iqr", fig.lab.size = 6)

Warning: Removed 3 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 3 rows containing non-finite outside the scale range (`stat_summary()`).
Warning: Removed 3 rows containing non-finite outside the scale range (`stat_compare_means()`).

ggsave(
  glue("{plot_folder}Violin_CTCF_lfc.pdf"),
  last_plot(),
  width = 5,
  height = 5
)

p <- ggboxplot(
  mdf,
  x = "variable",
  y = "value",
  fill = "class",
  palette = mypal
) + geom_hline(yintercept = 0, linetype = "dotted") + coord_cartesian(ylim =
                                                                        c(-2, 2))
annotate_figure(p, fig.lab = "DESEq foldchange mean treat vs mean mock, median+iqr", fig.lab.size = 6)

Warning: Removed 3 rows containing non-finite outside the scale range (`stat_boxplot()`).

ggsave(glue("{plot_folder}Boxplot_CTCF_lfc.pdf"), last_plot())

Saving 3 x 3 in image

mdf <- reshape2::melt(dplyr::select(results, c(
  "pro", "class", "deseq.lfc.pds", "deseq.lfc.pdc"
)))

Using pro, class as id variables

mdf$pro <- factor(mdf$pro, levels = c("Pro", "noPro"))
mdf$x <- as.factor(paste0(mdf$class, " ", mdf$variable))
mdf$x <- factor(mdf$x, levels = levels(mdf$x)[c(2, 1, 4, 3)])
p <- ggviolin(
  mdf,
  x = "x",
  y = "value",
  fill = "class",
  palette = mypal,
  add = "median_iqr",
  facet.by = "pro"
) + geom_hline(yintercept = 0, linetype = "dotted") + coord_cartesian(ylim =
                                                                        c(-2, 2)) + theme(axis.text.x = element_text(angle = 90, hjust = 1))
annotate_figure(p, fig.lab = "DESEq foldchange mean treat vs mean mock, median+iqr", fig.lab.size = 6)

Warning: Removed 3 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 3 rows containing non-finite outside the scale range (`stat_summary()`).

ggsave(glue("{plot_folder}Violin_CTCF_lfc_pro.pdf"), last_plot())

Saving 5 x 6 in image

med <- aggregate(deseq.lfc.pds ~ class,
                 data = results,
                 FUN = "median",
                 na.rm = T)
med$deseq.fc.pds <- 2 ^ med$deseq.lfc.pds
med

med <- aggregate(deseq.lfc.pds ~ name,
                 data = results,
                 FUN = "median",
                 na.rm = T)
med$deseq.fc.pds <- 2 ^ med$deseq.lfc.pds
med

med <- aggregate(deseq.lfc.pds ~ class,
                 data = results,
                 FUN = "median",
                 na.rm = T)
med$deseq.fc.pds <- 2 ^ med$deseq.lfc.pds
med

med <- aggregate(deseq.lfc.pdc ~ name,
                 data = results,
                 FUN = "median",
                 na.rm = T)
med$deseq.fc.pdc <- 2 ^ med$deseq.lfc.pdc
med

deseq_lfc_stats = compare_means(deseq.lfc.pds ~ class, data = results)
deseq_lfc_stats

write_tsv(deseq_lfc_stats,
          glue("{stat_output}pds-deseq2_lfc_statistics.tsv"))

deseq_lfc_stats = compare_means(deseq.lfc.pdc ~ class, data = results)
deseq_lfc_stats

write_tsv(deseq_lfc_stats,
          glue("{stat_output}phendc-deseq2_lfc_statistics.tsv"))

mdf <- reshape2::melt(dplyr::select(
  results,
  c(
    "class",
    "raw.lfc.pds_1",
    "raw.lfc.pds_2",
    "raw.lfc.pdc_1",
    "raw.lfc.pdc_2"
  )
))

Using class as id variables

ggviolin(
  mdf,
  x = "variable",
  y = "value",
  fill = "class",
  palette = mypal,
  add = "median_iqr"
) + geom_hline(yintercept = 0, linetype = "dotted") + coord_cartesian(ylim =
                                                                        c(-3, 3)) +
  stat_compare_means(aes(group = class), label.y = 3.6, size = 2)

Warning: Removed 469 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 469 rows containing non-finite outside the scale range (`stat_summary()`).
Warning: Removed 469 rows containing non-finite outside the scale range (`stat_compare_means()`).

ggsave(glue("{plot_folder}Violin_CTCF_lfc_individual_reps.pdf"), last_plot())

Saving 5 x 3 in image

Warning: Removed 469 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 469 rows containing non-finite outside the scale range (`stat_summary()`).
Warning: Removed 469 rows containing non-finite outside the scale range (`stat_compare_means()`).

ggdensity(
  results,
  x = "raw.lfc.pds",
  color = "class",
  fill = "class",
  palette = mypal
) + geom_vline(xintercept = 0, linetype = "dotted")

Warning: Removed 26 rows containing non-finite outside the scale range (`stat_density()`).

ggdensity(
  results,
  x = "raw.lfc.pdc",
  color = "class",
  fill = "class",
  palette = mypal
) + geom_vline(xintercept = 0, linetype = "dotted")

Warning: Removed 23 rows containing non-finite outside the scale range (`stat_density()`).

ggscatter(
  results,
  x = "log2.mock",
  y = "log2.pds",
  size = 1,shape=20,
  alpha = 0.1,
  color = "deseq.sig.pds",
  palette = mypal[c(5, 2)]
)

ggsave(glue("{plot_folder}Scatter_CTCF_DESEq_PDSvsMock.pdf"), rasterize(last_plot(),dpi = 600),width = 3, height= 3.2)

ggscatter(
  results,
  x = "log2.mock",
  y = "log2.pdc",
  size = 1,shape=20,
  alpha = 0.1,
  color = "deseq.sig.pdc",
  palette = mypal[c(5, 2)]
)

ggsave(glue("{plot_folder}Scatter_CTCF_DESEq_PhenDC3vsMock.pdf"), rasterize(last_plot(),dpi = 600),width = 3, height= 3.2)

tb <- table(results$class)
deseq.stats <- as.data.frame(t(as.matrix(tb)))
deseq.stats[1,] <- colSums(deseq.stats)
rownames(deseq.stats) <- c("Total")
deseq.stats.percent <- deseq.stats
deseq.stats.percent[1,] <- c(100,100)
tb

CTCF_and_G4 CTCF_not_G4 
       2288       49325 

tb <- table(results$deseq.sig.pds &
        (results$deseq.lfc.pds > 0),
      results$class)
deseq.stats <- rbind(deseq.stats, PDS.sig.up = as.data.frame.matrix(tb)[2,])
tb

       
        CTCF_and_G4 CTCF_not_G4
  FALSE        2220       46812
  TRUE           68        2510

tb <- prop.table(table(results$deseq.sig.pds &
        (results$deseq.lfc.pds > 0),
      results$class),margin = 2)*100
deseq.stats.percent <- rbind(deseq.stats.percent, PDS.sig.up  = as.data.frame.matrix(tb)[2,])
tb

       
        CTCF_and_G4 CTCF_not_G4
  FALSE   97.027972   94.910993
  TRUE     2.972028    5.089007

table(results$deseq.sig.pds &
        (results$deseq.lfc.pds > 0),
      results$class)

       
        CTCF_and_G4 CTCF_not_G4
  FALSE        2220       46812
  TRUE           68        2510

mdf <- reshape2::melt(table(
  results$deseq.sig.pds & (results$deseq.lfc.pds > 0),
  results$class
))
ggplot(mdf, aes(Var1, Var2, fill = value)) +
  geom_tile(show.legend = F) + geom_text(aes(label = value)) +
  scale_fill_gradient(low = "white", high = "orange") + theme_minimal()

vl <- list(
  sig = grep("TRUE", results$deseq.sigup.pds),
  CTCF_G4 = grep("and", results$class),
  CTCFonly = grep("not", results$class)
)
plot(euler(vl), quantities = T)

tb <- table(results$deseq.sig.pdc &
        (results$deseq.lfc.pdc > 0),
      results$class)
deseq.stats <- rbind(deseq.stats, PhenDC3.sig.up = as.data.frame.matrix(tb)[2,])
tb

       
        CTCF_and_G4 CTCF_not_G4
  FALSE        2251       48545
  TRUE           37         780

tb <- prop.table(table(results$deseq.sig.pdc &
        (results$deseq.lfc.pdc > 0),
      results$class),margin = 2)*100
deseq.stats.percent <- rbind(deseq.stats.percent, PhenDC3.sig.up = as.data.frame.matrix(tb)[2,])
tb

       
        CTCF_and_G4 CTCF_not_G4
  FALSE   98.382867   98.418652
  TRUE     1.617133    1.581348

table(results$deseq.sig.pdc &
        (results$deseq.lfc.pdc > 0),
      results$class)

       
        CTCF_and_G4 CTCF_not_G4
  FALSE        2251       48545
  TRUE           37         780

mdf <- reshape2::melt(table(
  results$deseq.sig.pdc & (results$deseq.lfc.pdc > 0),
  results$class
))
ggplot(mdf, aes(Var1, Var2, fill = value)) +
  geom_tile(show.legend = F) + geom_text(aes(label = value)) +
  scale_fill_gradient(low = "white", high = "orange") + theme_minimal()

results$uid <- seq(1:nrow(results))
vl <- list(
  sig = grep("TRUE", results$deseq.sigup.pdc),
  CTCF_G4 = grep("and", results$class),
  CTCFonly = grep("not", results$class)
)
plot(euler(vl), quantities = T)

table(results$deseq.sigup.pds, results$deseq.sigup.pdc)

       
        FALSE  TRUE
  FALSE 48576   456
  TRUE   2217   361

mdf <- reshape2::melt(table(results$deseq.sigup.pds, results$deseq.sigup.pdc))
ggplot(mdf, aes(Var1, Var2, fill = value)) +
  geom_tile(show.legend = F) + geom_text(aes(label = value)) +
  scale_fill_gradient(low = "white", high = "orange") + theme_minimal()

tb <- table(results$deseq.sigup.pds & results$deseq.sigup.pdc,
      results$class)
deseq.stats <- rbind(deseq.stats, both.sig.up = as.data.frame.matrix(tb)[2,])
tb

       
        CTCF_and_G4 CTCF_not_G4
  FALSE        2277       48975
  TRUE           11         350

tb <- prop.table(table(results$deseq.sigup.pds & results$deseq.sigup.pdc,
      results$class),margin = 2)*100
deseq.stats.percent <- rbind(deseq.stats.percent, both = as.data.frame.matrix(tb)[2,])
tb

       
        CTCF_and_G4 CTCF_not_G4
  FALSE  99.5192308  99.2904207
  TRUE    0.4807692   0.7095793

table(results$deseq.sigup.pds & results$deseq.sigup.pdc, results$class)

       
        CTCF_and_G4 CTCF_not_G4
  FALSE        2277       48975
  TRUE           11         350

mdf <- reshape2::melt(table(results$deseq.sigup.pds & results$deseq.sigup.pdc, results$class))
ggplot(mdf, aes(Var1, Var2, fill = value)) +
  geom_tile(show.legend = F) + geom_text(aes(label = value)) +
  scale_fill_gradient(low = "white", high = "orange") + theme_minimal()

deseq.stats$class <- rownames(deseq.stats) 
mdf <- reshape2::melt(deseq.stats)

Using class as id variables

ggplot(mdf, aes(variable, class, fill = value)) +
  geom_tile(show.legend = F) + geom_text(aes(label = value)) +
  scale_fill_gradient(low = "white", high = "orange") + theme_minimal()

ggsave(glue("{plot_folder}Table_CTCF_DESEq_Sigup.pdf"), rasterize(last_plot(),dpi = 600),width = 2.5, height= 2.5)

deseq.stats.percent$class <- rownames(deseq.stats.percent) 
mdf <- reshape2::melt(deseq.stats.percent[-1,])

Using class as id variables

ggplot(mdf, aes(variable, class, fill = value)) +
  geom_tile(show.legend = F) + geom_text(aes(label = round(mdf$value,2))) +
  scale_fill_gradient(low = "white", high = "orange") + theme_minimal()

Warning: Use of `mdf$value` is discouraged.
ℹ Use `value` instead.

ggsave(glue("{plot_folder}Table_CTCF_DESEq_Sigup_percent.pdf"), rasterize(last_plot(),dpi = 600),width = 2.5, height= 2.5)

Warning: Use of `mdf$value` is discouraged.
ℹ Use `value` instead.

vl <- list(
  sig_PDS = grep("TRUE", results$deseq.sigup.pds),
  sig_PDC = grep("TRUE", results$deseq.sigup.pdc),
  CTCF_G4 = grep("and", results$class),
  CTCFonly = grep("not", results$class)
)
plot(euler(vl), quantities = T)

results$uid <- seq(1:nrow(results))
vl <- list(
  sig_PDS = grep("TRUE", results$deseq.sigup.pds),
  sig_PDC = grep("TRUE", results$deseq.sigup.pdc),
  CTCF_G4 = grep("and", results$class)
)
plot(euler(vl), quantities = T)

results$sig.by.class.pds <- paste0(results$deseq.sigup.pds, "_", results$class)
results$psize <- 0.01
results$psize[results$deseq.sigup.pds &
                results$class == "CTCF_and_G4"] <- 1

ggscatter(
  results,
  x = "log2.mock",
  y = "log2.pds",
  size = 0.5,
  alpha = results$psize,
  color = "sig.by.class.pds",
  palette = c(mypal[5], mypal[5], mypal[5], mypal[2], mypal[1])
)

ggscatter(
  results[!grepl("NA", results$sig.by.class.pds), ],
  x = "log2.mock",
  y = "deseq.lfc.pds",
  size = 0.2,
  alpha = "psize",
  color = "sig.by.class.pds",
  palette = c("#505050", "#505050", "red2", "blue")
)

ggscatterhist(
  results[!grepl("NA", results$sig.by.class.pds), ],
  x = "log2.mock",
  y = "log2.pds",
  size = 0.4,
  alpha = "psize",
  color = "sig.by.class.pds",
  margin.params = list(
    fill = "sig.by.class.pds",
    color = "black",
    size = 0.2
  ),
  palette = c("#505050", "#505050", "red2", "blue")
)

Warning: Removed 13 rows containing non-finite outside the scale range (`stat_density()`).
Warning: Removed 10 rows containing non-finite outside the scale range (`stat_density()`).

ggscatter(
  results,
  x = "raw.lfc.pds",
  y = "log2.G4",
  size = 0.2,
  alpha = 0.1,
  color = "deseq.sig.pds",
  cor.coef = T,
  palette = c("#888888",mypal[2])
)

Warning: Removed 16803 rows containing non-finite outside the scale range (`stat_cor()`).
Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`).

ggsave(glue("{plot_folder}Scatter_G4_vs_LFC_PDS.pdf"),
       plot = rasterize(last_plot()))

Saving 3 x 3 in image

Warning: Removed 16803 rows containing non-finite outside the scale range (`stat_cor()`).
Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`).

ggscatter(
  results,
  x = "raw.lfc.pdc",
  y = "log2.G4",
  size = 0.2,
  alpha = 0.1,
  color = "deseq.sig.pdc",
  cor.coef = T,
  palette = c("#888888",mypal[2])
)

Warning: Removed 16800 rows containing non-finite outside the scale range (`stat_cor()`).

ggsave(glue("{plot_folder}Scatter_G4_vs_LFC_PDC.pdf"),
       plot = rasterize(last_plot()))

Saving 3 x 3 in image

Warning: Removed 16800 rows containing non-finite outside the scale range (`stat_cor()`).

results$G4.quantile <- dplyr::ntile(results$G4_NT, n = 5)
results$pds.quantile <- dplyr::ntile(results$mean.pds-results$mean.mock, n = 4)
results$pdc.quantile <- dplyr::ntile(results$mean.pdc-results$mean.mock, n = 4)

top25.pds <- makeGRangesFromDataFrame(results[results$pds.quantile==4,1:3],na.rm=T)
bot75.pds <- makeGRangesFromDataFrame(results[results$pds.quantile!=4,1:3],na.rm=T)
top25.pds.CTCF_G4 <- makeGRangesFromDataFrame(results[(results$pds.quantile==4 & results$class == "CTCF_and_G4"),1:3],na.rm=T)
top25.pds.CTCF_only <- makeGRangesFromDataFrame(results[(results$pds.quantile==4  &  results$class == "CTCF_not_G4"),1:3],na.rm=T)

vl <- list(
  CTCF_G4 = top25.pds.CTCF_G4,
  CTCF_only = top25.pds.CTCF_only,
  G4motif = rtracklayer::import("../peaks/mm10_canonical_G4_PQS-regex.bed")
)
bedscout::plot_euler(grlist = vl,names = c("CTCF_G4","CTCF_only","G4motif"))

ggviolin(
  results,
  x = "pds.quantile",
  y = "deseq.lfc.pds",
  fill = mypal[3],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-1.5, 1.5)) + geom_hline(yintercept = 0, linetype =
                                                    "dotted")

Warning: Removed 3 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 3 rows containing non-finite outside the scale range (`stat_summary()`).

ggsave(glue("{plot_folder}Violin_lfcPDS_by_PDSquantile.pdf"),
       plot = last_plot())

Saving 3 x 3 in image

Warning: Removed 3 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 3 rows containing non-finite outside the scale range (`stat_summary()`).

ggviolin(
  results,
  x = "pdc.quantile",
  y = "deseq.lfc.pdc",
  fill = mypal[3],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-1.5, 1.5)) + geom_hline(yintercept = 0, linetype =
                                                    "dotted")

ggsave(glue("{plot_folder}Violin_lfcPDS_by_PhenDC3quantile.pdf"),
       plot = last_plot())

Saving 3 x 3 in image

tb <- table(results$pds.quantile, results$class)
tb

   
    CTCF_and_G4 CTCF_not_G4
  1         540       12364
  2         639       12264
  3         552       12351
  4         557       12346

ggbarplot(as.data.frame(t(as.matrix(tb))),"Var2","Freq",fill="Var1",palette = c(mypal[1],"#aaaaaa"),label = TRUE, lab.pos="in",ylim=c(11000,13000))

ggsave(glue("{plot_folder}Barplot_peakCat_by_PDSquantile.pdf"),
       plot = last_plot())

Saving 4 x 3 in image

tb <- table(results$pdc.quantile, results$class)
tb

   
    CTCF_and_G4 CTCF_not_G4
  1         279       12625
  2         614       12289
  3         615       12288
  4         780       12123

ggbarplot(as.data.frame(t(as.matrix(tb))),"Var2","Freq",fill="Var1",palette = c(mypal[1],"#aaaaaa"),label = TRUE, lab.pos="in",ylim=c(11000,13000))

ggsave(glue("{plot_folder}Barplot_peakCat_by_PhenDC3quantile.pdf"),
       plot = last_plot())

Saving 4 x 3 in image

p1 <- plot_bw_profile(bwfiles = geo_bigwigs,loci = top25.pds, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,6))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 658 generated ( 0.0509958924281175 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 658 generated ( 0.0509958924281175 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 658 generated ( 0.0509958924281175 per locus)

p2 <- plot_bw_profile(bwfiles = geo_bigwigs,loci = bot75.pds, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,6))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 2056 generated ( 0.0531128907259106 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 2056 generated ( 0.0531128907259106 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 2056 generated ( 0.0531128907259106 per locus)

ggarrange(p1,p2, ncol=2)

ggsave(glue("{plot_folder}Profile_CTCF_top25_PDSquantile.pdf"),
       plot = last_plot())

Saving 6 x 3 in image

top25.pdc <- makeGRangesFromDataFrame(results[results$pdc.quantile==4,1:3],na.rm=T)
bot75.pdc <- makeGRangesFromDataFrame(results[results$pdc.quantile!=4,1:3],na.rm=T)
p1 <- plot_bw_profile(bwfiles = geo_bigwigs,loci = top25.pdc, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,6))
p2 <- plot_bw_profile(bwfiles = geo_bigwigs,loci = bot75.pdc, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,6))
ggarrange(p1,p2, ncol=2)
ggsave(glue("{plot_folder}Profile_CTCF_top25_PhenDC3quantile.pdf"),
       plot = last_plot())

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[1:2],loci = top25.pds.CTCF_G4, mode = "center",verbose = F, colors = mypal[c(1,2)]) + coord_cartesian(ylim=c(0,10))
p2 <- plot_bw_profile(bwfiles = geo_bigwigs[1:2],loci = top25.pds.CTCF_only, mode = "center",verbose = F, colors = mypal[c(1,2)]) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 639 generated ( 0.0517576543009882 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 639 generated ( 0.0517576543009882 per locus)

ggarrange(p1,p2, ncol=2)

ggsave(glue("{plot_folder}Profile_CTCF_top25_PDSquantile_byG4overlap.pdf"),
       plot = last_plot())

Saving 6 x 3 in image

top25.pdc.CTCF_G4 <- makeGRangesFromDataFrame(results[(results$pdc.quantile==4 & results$class == "CTCF_and_G4"),1:3],na.rm=T)
top25.pdc.CTCF_only <- makeGRangesFromDataFrame(results[(results$pdc.quantile==4  &  results$class == "CTCF_not_G4"),1:3],na.rm=T)

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[c(1,3)],loci = top25.pdc.CTCF_G4, mode = "center",verbose = F, colors = mypal[c(1,3)]) + coord_cartesian(ylim=c(0,10))
p2 <- plot_bw_profile(bwfiles = geo_bigwigs[c(1,3)],loci = top25.pdc.CTCF_only, mode = "center",verbose = F, colors = mypal[c(1,3)]) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 584 generated ( 0.0481728944980615 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 584 generated ( 0.0481728944980615 per locus)

ggarrange(p1,p2, ncol=2)

ggsave(glue("{plot_folder}Profile_CTCF_top25_PhenDC3quantile_byG4overlap.pdf"),
       plot = last_plot())

Saving 6 x 3 in image

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[2],bg_bwfiles = geo_bigwigs[1], loci = top25.pds.CTCF_G4, mode = "center",verbose = F, colors = mypal[2],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in plot_bw_profile(bwfiles = geo_bigwigs[2], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

p2 <- plot_bw_profile(bwfiles = geo_bigwigs[2],bg_bwfiles = geo_bigwigs[1], loci = top25.pds.CTCF_only, mode = "center",verbose = F, colors = mypal[2],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 639 generated ( 0.0517576543009882 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 639 generated ( 0.0517576543009882 per locus)
Warning in plot_bw_profile(bwfiles = geo_bigwigs[2], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

ggarrange(p1,p2, ncol=2)

ggsave(glue("{plot_folder}Profile_CTCFfoldchange_top25_PDSquantile_byG4.pdf"),
       plot = last_plot())

Saving 6 x 3 in image

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[3],bg_bwfiles = geo_bigwigs[1], loci = top25.pdc.CTCF_G4, mode = "center",verbose = F, colors = mypal[3],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in plot_bw_profile(bwfiles = geo_bigwigs[3], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

p2 <- plot_bw_profile(bwfiles = geo_bigwigs[3],bg_bwfiles = geo_bigwigs[1], loci = top25.pdc.CTCF_only, mode = "center",verbose = F, colors = mypal[3],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 584 generated ( 0.0481728944980615 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 584 generated ( 0.0481728944980615 per locus)
Warning in plot_bw_profile(bwfiles = geo_bigwigs[3], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

ggarrange(p1,p2, ncol=2)

ggsave(glue("{plot_folder}Profile_CTCFfoldchange_top25_PhenDC3quantile_byG4.pdf"),
       plot = last_plot())

Saving 6 x 3 in image

p1 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[1:2], loci = top25.pds.CTCF_G4, mode = "center",verbose = F, colors = mypal,show_error = T) + coord_cartesian(ylim=c(0,15))
p2 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[1:2], loci = top25.pds.CTCF_only, mode = "center",verbose = F, colors = mypal,show_error = T) + coord_cartesian(ylim=c(0,15))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 639 generated ( 0.0517576543009882 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 639 generated ( 0.0517576543009882 per locus)

p3 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[1:2], loci = "../peaks/Control_peaks_shuffled.bed", mode = "center",verbose = F, colors = mypal,show_error = T) + coord_cartesian(ylim=c(0,15))

Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55177489-55182488)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59791468-59796467)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34554102-34559101)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2976368-2981367)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4605202-4610201)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156306583-156311582)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51509139-51514138)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52236792-52241791)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3553304-3558303)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180066874-180071873)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56795314-56800313)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1031217-1036216)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:362354-367353)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83220148-83225147)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46595524-46600523)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3470832-3475831)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1672470-1677469)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26031987-26036986)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85286610-85291609)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:669697-674696)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63137543-63142542)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2629620-2634619)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11577826-11582825)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27473093-27478092)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43352103-43357102)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14124041-14129040)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2016278-2021277)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71822176-71827175)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90689200-90694199)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85179774-85184773)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8737856-8742855)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28182348-28187347)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42218540-42223539)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61904103-61909102)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:699055-704054)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35280798-35285797)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21643087-21648086)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19784876-19789875)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1645906-1650905)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:636479-641478)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31204931-31209930)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:540267-545266)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112808590-112813589)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1580419-1585418)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67033138-67038137)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2250907-2255906)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:437800-442799)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1932398-1937397)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73694467-73699466)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38467783-38472782)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45578258-45583257)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19330970-19335969)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72043389-72048388)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2350848-2355847)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23625981-23630980)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35804360-35809359)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2251022-2256021)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15955322-15960321)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71734668-71739667)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46754365-46759364)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17279686-17284685)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79743893-79748892)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75425910-75430909)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2345208-2350207)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44767980-44772979)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13173181-13178180)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22298239-22303238)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4869526-4874525)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1976323-1981322)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71105870-71110869)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22335476-22340475)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32417122-32422121)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175744072-175749071)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:705832-710831)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170469887-170474886)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94978304-94983303)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67606331-67611330)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81108849-81113848)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5157828-5162827)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28470520-28475519)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11915790-11920789)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69232280-69237279)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3529157-3534156)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4153351-4158350)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:582754-587753)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75054172-75059171)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19017559-19022558)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72282149-72287148)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31203993-31208992)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75453219-75458218)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23230994-23235993)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30776138-30781137)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34167438-34172437)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63217594-63222593)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51286044-51291043)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35500989-35505988)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36433441-36438440)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48706372-48711371)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20393428-20398427)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7072056-7077055)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3781198-3786197)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51888917-51893916)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6761874-6766873)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13194144-13199143)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21366283-21371282)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74939193-74944192)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5593190-5598189)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100800043-100805042)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51499951-51504950)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33141446-33146445)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77739308-77744307)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26381239-26386238)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89800657-89805656)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 6082 generated ( 4.67846153846154 per locus)
Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55177489-55182488)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59791468-59796467)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34554102-34559101)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2976368-2981367)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4605202-4610201)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156306583-156311582)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51509139-51514138)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52236792-52241791)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3553304-3558303)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180066874-180071873)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56795314-56800313)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1031217-1036216)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:362354-367353)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83220148-83225147)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46595524-46600523)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3470832-3475831)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1672470-1677469)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26031987-26036986)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85286610-85291609)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:669697-674696)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63137543-63142542)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2629620-2634619)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11577826-11582825)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27473093-27478092)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43352103-43357102)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14124041-14129040)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2016278-2021277)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71822176-71827175)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90689200-90694199)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85179774-85184773)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8737856-8742855)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28182348-28187347)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42218540-42223539)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61904103-61909102)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:699055-704054)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35280798-35285797)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21643087-21648086)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19784876-19789875)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1645906-1650905)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:636479-641478)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31204931-31209930)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:540267-545266)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112808590-112813589)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1580419-1585418)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67033138-67038137)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2250907-2255906)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:437800-442799)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1932398-1937397)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73694467-73699466)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38467783-38472782)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45578258-45583257)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19330970-19335969)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72043389-72048388)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2350848-2355847)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23625981-23630980)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35804360-35809359)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2251022-2256021)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15955322-15960321)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71734668-71739667)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46754365-46759364)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17279686-17284685)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79743893-79748892)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75425910-75430909)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2345208-2350207)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44767980-44772979)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13173181-13178180)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22298239-22303238)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4869526-4874525)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1976323-1981322)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71105870-71110869)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22335476-22340475)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32417122-32422121)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175744072-175749071)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:705832-710831)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170469887-170474886)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94978304-94983303)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67606331-67611330)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81108849-81113848)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5157828-5162827)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28470520-28475519)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11915790-11920789)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69232280-69237279)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3529157-3534156)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4153351-4158350)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:582754-587753)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75054172-75059171)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19017559-19022558)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72282149-72287148)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31203993-31208992)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75453219-75458218)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23230994-23235993)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30776138-30781137)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34167438-34172437)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63217594-63222593)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51286044-51291043)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35500989-35505988)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36433441-36438440)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48706372-48711371)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20393428-20398427)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7072056-7077055)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3781198-3786197)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51888917-51893916)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6761874-6766873)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13194144-13199143)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21366283-21371282)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74939193-74944192)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5593190-5598189)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100800043-100805042)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51499951-51504950)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33141446-33146445)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77739308-77744307)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26381239-26386238)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89800657-89805656)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 6082 generated ( 4.67846153846154 per locus)

ggarrange(p1,p2,p3, ncol=3)

p1 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[2], bg_bwfiles = geo_CnR_bigwigs[1], norm_mode = "log2fc", loci = top25.pds.CTCF_G4, mode = "center",verbose = F, colors = mypal[2],show_error = T) + coord_cartesian(ylim=c(-2,2))

Warning in plot_bw_profile(bwfiles = geo_CnR_bigwigs[2], bg_bwfiles = geo_CnR_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

p2 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[2], bg_bwfiles = geo_CnR_bigwigs[1], norm_mode = "log2fc", loci = top25.pds.CTCF_only, mode = "center",verbose = F, colors = mypal[2],show_error = T) + coord_cartesian(ylim=c(-2,2))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 639 generated ( 0.0517576543009882 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 639 generated ( 0.0517576543009882 per locus)
Warning in plot_bw_profile(bwfiles = geo_CnR_bigwigs[2], bg_bwfiles = geo_CnR_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

p3 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[2], bg_bwfiles = geo_CnR_bigwigs[1], norm_mode = "log2fc", loci = "../peaks/Control_peaks_shuffled.bed", mode = "center",verbose = F, colors = mypal[2],show_error = T) + coord_cartesian(ylim=c(-2,2))

Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55177489-55182488)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59791468-59796467)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34554102-34559101)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2976368-2981367)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4605202-4610201)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156306583-156311582)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51509139-51514138)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52236792-52241791)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3553304-3558303)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180066874-180071873)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56795314-56800313)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1031217-1036216)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:362354-367353)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83220148-83225147)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46595524-46600523)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3470832-3475831)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1672470-1677469)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26031987-26036986)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85286610-85291609)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:669697-674696)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63137543-63142542)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2629620-2634619)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11577826-11582825)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27473093-27478092)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43352103-43357102)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14124041-14129040)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2016278-2021277)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71822176-71827175)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90689200-90694199)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85179774-85184773)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8737856-8742855)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28182348-28187347)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42218540-42223539)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61904103-61909102)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:699055-704054)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35280798-35285797)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21643087-21648086)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19784876-19789875)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1645906-1650905)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:636479-641478)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31204931-31209930)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:540267-545266)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112808590-112813589)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1580419-1585418)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67033138-67038137)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2250907-2255906)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:437800-442799)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1932398-1937397)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73694467-73699466)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38467783-38472782)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45578258-45583257)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19330970-19335969)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72043389-72048388)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2350848-2355847)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23625981-23630980)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35804360-35809359)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2251022-2256021)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15955322-15960321)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71734668-71739667)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46754365-46759364)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17279686-17284685)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79743893-79748892)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75425910-75430909)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2345208-2350207)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44767980-44772979)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13173181-13178180)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22298239-22303238)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4869526-4874525)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1976323-1981322)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71105870-71110869)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22335476-22340475)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32417122-32422121)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175744072-175749071)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:705832-710831)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170469887-170474886)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94978304-94983303)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67606331-67611330)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81108849-81113848)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5157828-5162827)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28470520-28475519)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11915790-11920789)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69232280-69237279)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3529157-3534156)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4153351-4158350)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:582754-587753)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75054172-75059171)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19017559-19022558)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72282149-72287148)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31203993-31208992)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75453219-75458218)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23230994-23235993)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30776138-30781137)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34167438-34172437)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63217594-63222593)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51286044-51291043)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35500989-35505988)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36433441-36438440)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48706372-48711371)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20393428-20398427)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7072056-7077055)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3781198-3786197)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51888917-51893916)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6761874-6766873)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13194144-13199143)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21366283-21371282)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74939193-74944192)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5593190-5598189)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100800043-100805042)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51499951-51504950)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33141446-33146445)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77739308-77744307)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26381239-26386238)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89800657-89805656)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 6082 generated ( 4.67846153846154 per locus)
Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55177489-55182488)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59791468-59796467)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34554102-34559101)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2976368-2981367)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4605202-4610201)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156306583-156311582)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51509139-51514138)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52236792-52241791)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3553304-3558303)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180066874-180071873)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56795314-56800313)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1031217-1036216)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:362354-367353)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83220148-83225147)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46595524-46600523)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3470832-3475831)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1672470-1677469)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26031987-26036986)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85286610-85291609)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:669697-674696)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63137543-63142542)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2629620-2634619)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11577826-11582825)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27473093-27478092)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43352103-43357102)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14124041-14129040)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2016278-2021277)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71822176-71827175)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90689200-90694199)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85179774-85184773)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8737856-8742855)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28182348-28187347)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42218540-42223539)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61904103-61909102)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:699055-704054)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35280798-35285797)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21643087-21648086)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19784876-19789875)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1645906-1650905)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:636479-641478)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31204931-31209930)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:540267-545266)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112808590-112813589)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1580419-1585418)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67033138-67038137)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2250907-2255906)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:437800-442799)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1932398-1937397)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73694467-73699466)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38467783-38472782)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45578258-45583257)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19330970-19335969)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72043389-72048388)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2350848-2355847)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23625981-23630980)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35804360-35809359)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2251022-2256021)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15955322-15960321)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71734668-71739667)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46754365-46759364)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17279686-17284685)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79743893-79748892)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75425910-75430909)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2345208-2350207)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44767980-44772979)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13173181-13178180)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22298239-22303238)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4869526-4874525)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1976323-1981322)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71105870-71110869)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22335476-22340475)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32417122-32422121)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175744072-175749071)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:705832-710831)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170469887-170474886)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94978304-94983303)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67606331-67611330)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81108849-81113848)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5157828-5162827)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28470520-28475519)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11915790-11920789)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69232280-69237279)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3529157-3534156)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4153351-4158350)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:582754-587753)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75054172-75059171)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19017559-19022558)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72282149-72287148)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31203993-31208992)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75453219-75458218)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23230994-23235993)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30776138-30781137)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34167438-34172437)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63217594-63222593)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51286044-51291043)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35500989-35505988)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36433441-36438440)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48706372-48711371)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20393428-20398427)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7072056-7077055)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3781198-3786197)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51888917-51893916)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6761874-6766873)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13194144-13199143)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21366283-21371282)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74939193-74944192)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5593190-5598189)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100800043-100805042)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51499951-51504950)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33141446-33146445)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77739308-77744307)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26381239-26386238)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89800657-89805656)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 6082 generated ( 4.67846153846154 per locus)
Warning in plot_bw_profile(bwfiles = geo_CnR_bigwigs[2], bg_bwfiles = geo_CnR_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

ggarrange(p1,p2,p3, ncol=3)

p1 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[3:4], loci = top25.pdc.CTCF_G4, mode = "center",verbose = F, colors = mypal,show_error = T) + coord_cartesian(ylim=c(0,15))
p2 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[3:4], loci = top25.pdc.CTCF_only, mode = "center",verbose = F, colors = mypal,show_error = T) + coord_cartesian(ylim=c(0,15))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 584 generated ( 0.0481728944980615 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 584 generated ( 0.0481728944980615 per locus)

p3 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[3:4], loci = "../peaks/Control_peaks_shuffled.bed", mode = "center",verbose = F, colors = mypal,show_error = T) + coord_cartesian(ylim=c(0,15))

Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55177489-55182488)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59791468-59796467)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34554102-34559101)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2976368-2981367)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4605202-4610201)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156306583-156311582)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51509139-51514138)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52236792-52241791)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3553304-3558303)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180066874-180071873)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56795314-56800313)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1031217-1036216)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:362354-367353)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83220148-83225147)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46595524-46600523)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3470832-3475831)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1672470-1677469)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26031987-26036986)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85286610-85291609)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:669697-674696)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63137543-63142542)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2629620-2634619)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11577826-11582825)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27473093-27478092)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43352103-43357102)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14124041-14129040)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2016278-2021277)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71822176-71827175)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90689200-90694199)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85179774-85184773)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8737856-8742855)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28182348-28187347)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42218540-42223539)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61904103-61909102)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:699055-704054)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35280798-35285797)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21643087-21648086)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19784876-19789875)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1645906-1650905)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:636479-641478)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31204931-31209930)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:540267-545266)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112808590-112813589)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1580419-1585418)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67033138-67038137)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2250907-2255906)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:437800-442799)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1932398-1937397)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73694467-73699466)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38467783-38472782)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45578258-45583257)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19330970-19335969)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72043389-72048388)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2350848-2355847)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23625981-23630980)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35804360-35809359)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2251022-2256021)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15955322-15960321)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71734668-71739667)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46754365-46759364)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17279686-17284685)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79743893-79748892)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75425910-75430909)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2345208-2350207)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44767980-44772979)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13173181-13178180)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22298239-22303238)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4869526-4874525)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1976323-1981322)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71105870-71110869)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22335476-22340475)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32417122-32422121)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175744072-175749071)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:705832-710831)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170469887-170474886)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94978304-94983303)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67606331-67611330)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81108849-81113848)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5157828-5162827)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28470520-28475519)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11915790-11920789)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69232280-69237279)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3529157-3534156)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4153351-4158350)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:582754-587753)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75054172-75059171)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19017559-19022558)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72282149-72287148)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31203993-31208992)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75453219-75458218)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23230994-23235993)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30776138-30781137)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34167438-34172437)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63217594-63222593)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51286044-51291043)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35500989-35505988)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36433441-36438440)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48706372-48711371)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20393428-20398427)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7072056-7077055)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3781198-3786197)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51888917-51893916)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6761874-6766873)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13194144-13199143)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21366283-21371282)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74939193-74944192)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5593190-5598189)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100800043-100805042)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51499951-51504950)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33141446-33146445)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77739308-77744307)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26381239-26386238)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89800657-89805656)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 6082 generated ( 4.67846153846154 per locus)
Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55177489-55182488)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59791468-59796467)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34554102-34559101)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2976368-2981367)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4605202-4610201)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156306583-156311582)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51509139-51514138)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52236792-52241791)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3553304-3558303)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180066874-180071873)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56795314-56800313)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1031217-1036216)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:362354-367353)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83220148-83225147)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46595524-46600523)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3470832-3475831)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1672470-1677469)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26031987-26036986)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85286610-85291609)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:669697-674696)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63137543-63142542)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2629620-2634619)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11577826-11582825)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27473093-27478092)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43352103-43357102)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14124041-14129040)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2016278-2021277)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71822176-71827175)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90689200-90694199)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85179774-85184773)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8737856-8742855)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28182348-28187347)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42218540-42223539)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61904103-61909102)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:699055-704054)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35280798-35285797)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21643087-21648086)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19784876-19789875)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1645906-1650905)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:636479-641478)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31204931-31209930)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:540267-545266)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112808590-112813589)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1580419-1585418)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67033138-67038137)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2250907-2255906)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:437800-442799)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1932398-1937397)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73694467-73699466)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38467783-38472782)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45578258-45583257)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19330970-19335969)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72043389-72048388)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2350848-2355847)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23625981-23630980)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35804360-35809359)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2251022-2256021)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15955322-15960321)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71734668-71739667)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46754365-46759364)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17279686-17284685)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79743893-79748892)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75425910-75430909)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2345208-2350207)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44767980-44772979)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13173181-13178180)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22298239-22303238)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4869526-4874525)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1976323-1981322)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71105870-71110869)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22335476-22340475)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32417122-32422121)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175744072-175749071)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:705832-710831)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170469887-170474886)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94978304-94983303)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67606331-67611330)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81108849-81113848)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5157828-5162827)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28470520-28475519)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11915790-11920789)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69232280-69237279)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3529157-3534156)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4153351-4158350)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:582754-587753)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75054172-75059171)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19017559-19022558)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72282149-72287148)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31203993-31208992)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75453219-75458218)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23230994-23235993)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30776138-30781137)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34167438-34172437)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63217594-63222593)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51286044-51291043)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35500989-35505988)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36433441-36438440)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48706372-48711371)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20393428-20398427)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7072056-7077055)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3781198-3786197)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51888917-51893916)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6761874-6766873)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13194144-13199143)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21366283-21371282)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74939193-74944192)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5593190-5598189)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100800043-100805042)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51499951-51504950)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33141446-33146445)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77739308-77744307)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26381239-26386238)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89800657-89805656)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 6082 generated ( 4.67846153846154 per locus)

ggarrange(p1,p2,p3, ncol=3)

p1 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[4], bg_bwfiles = geo_CnR_bigwigs[3], norm_mode = "log2fc", loci = top25.pdc.CTCF_G4, mode = "center",verbose = F, colors = mypal[2],show_error = T) + coord_cartesian(ylim=c(-2,2))

Warning in plot_bw_profile(bwfiles = geo_CnR_bigwigs[4], bg_bwfiles = geo_CnR_bigwigs[3],  :
  Stderr estimate not available when normalizing by input

p2 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[4], bg_bwfiles = geo_CnR_bigwigs[3], norm_mode = "log2fc", loci = top25.pdc.CTCF_only, mode = "center",verbose = F, colors = mypal[2],show_error = T) + coord_cartesian(ylim=c(-2,2))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 584 generated ( 0.0481728944980615 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 584 generated ( 0.0481728944980615 per locus)
Warning in plot_bw_profile(bwfiles = geo_CnR_bigwigs[4], bg_bwfiles = geo_CnR_bigwigs[3],  :
  Stderr estimate not available when normalizing by input

p3 <- plot_bw_profile(bwfiles = geo_CnR_bigwigs[4], bg_bwfiles = geo_CnR_bigwigs[3], norm_mode = "log2fc", loci = "../peaks/Control_peaks_shuffled.bed", mode = "center",verbose = F, colors = mypal[2],show_error = T) + coord_cartesian(ylim=c(-2,2))

Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55177489-55182488)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59791468-59796467)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34554102-34559101)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2976368-2981367)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4605202-4610201)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156306583-156311582)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51509139-51514138)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52236792-52241791)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3553304-3558303)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180066874-180071873)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56795314-56800313)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1031217-1036216)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:362354-367353)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83220148-83225147)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46595524-46600523)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3470832-3475831)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1672470-1677469)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26031987-26036986)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85286610-85291609)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:669697-674696)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63137543-63142542)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2629620-2634619)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11577826-11582825)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27473093-27478092)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43352103-43357102)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14124041-14129040)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2016278-2021277)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71822176-71827175)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90689200-90694199)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85179774-85184773)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8737856-8742855)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28182348-28187347)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42218540-42223539)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61904103-61909102)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:699055-704054)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35280798-35285797)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21643087-21648086)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19784876-19789875)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1645906-1650905)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:636479-641478)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31204931-31209930)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:540267-545266)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112808590-112813589)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1580419-1585418)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67033138-67038137)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2250907-2255906)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:437800-442799)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1932398-1937397)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73694467-73699466)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38467783-38472782)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45578258-45583257)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19330970-19335969)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72043389-72048388)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2350848-2355847)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23625981-23630980)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35804360-35809359)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2251022-2256021)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15955322-15960321)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71734668-71739667)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46754365-46759364)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17279686-17284685)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79743893-79748892)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75425910-75430909)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2345208-2350207)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44767980-44772979)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13173181-13178180)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22298239-22303238)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4869526-4874525)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1976323-1981322)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71105870-71110869)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22335476-22340475)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32417122-32422121)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175744072-175749071)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:705832-710831)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170469887-170474886)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94978304-94983303)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67606331-67611330)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81108849-81113848)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5157828-5162827)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28470520-28475519)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11915790-11920789)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69232280-69237279)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3529157-3534156)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4153351-4158350)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:582754-587753)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75054172-75059171)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19017559-19022558)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72282149-72287148)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31203993-31208992)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75453219-75458218)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23230994-23235993)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30776138-30781137)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34167438-34172437)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63217594-63222593)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51286044-51291043)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35500989-35505988)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36433441-36438440)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48706372-48711371)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20393428-20398427)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7072056-7077055)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3781198-3786197)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51888917-51893916)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6761874-6766873)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13194144-13199143)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21366283-21371282)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74939193-74944192)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5593190-5598189)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100800043-100805042)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51499951-51504950)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33141446-33146445)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77739308-77744307)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26381239-26386238)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89800657-89805656)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 6082 generated ( 4.67846153846154 per locus)
Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55177489-55182488)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59791468-59796467)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34554102-34559101)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2976368-2981367)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4605202-4610201)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156306583-156311582)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51509139-51514138)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52236792-52241791)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3553304-3558303)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180066874-180071873)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56795314-56800313)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1031217-1036216)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:362354-367353)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83220148-83225147)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46595524-46600523)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3470832-3475831)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1672470-1677469)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26031987-26036986)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85286610-85291609)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:669697-674696)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63137543-63142542)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2629620-2634619)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11577826-11582825)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27473093-27478092)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43352103-43357102)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14124041-14129040)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2016278-2021277)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71822176-71827175)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90689200-90694199)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85179774-85184773)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8737856-8742855)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28182348-28187347)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42218540-42223539)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61904103-61909102)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:699055-704054)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35280798-35285797)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21643087-21648086)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19784876-19789875)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1645906-1650905)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:636479-641478)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31204931-31209930)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:540267-545266)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112808590-112813589)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1580419-1585418)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67033138-67038137)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2250907-2255906)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:437800-442799)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1932398-1937397)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73694467-73699466)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38467783-38472782)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45578258-45583257)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19330970-19335969)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72043389-72048388)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2350848-2355847)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23625981-23630980)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35804360-35809359)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2251022-2256021)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15955322-15960321)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71734668-71739667)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46754365-46759364)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17279686-17284685)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79743893-79748892)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75425910-75430909)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2345208-2350207)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44767980-44772979)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13173181-13178180)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22298239-22303238)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4869526-4874525)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1976323-1981322)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71105870-71110869)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22335476-22340475)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32417122-32422121)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175744072-175749071)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:705832-710831)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170469887-170474886)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94978304-94983303)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67606331-67611330)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81108849-81113848)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5157828-5162827)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28470520-28475519)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11915790-11920789)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69232280-69237279)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3529157-3534156)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4153351-4158350)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:582754-587753)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75054172-75059171)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19017559-19022558)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72282149-72287148)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31203993-31208992)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75453219-75458218)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23230994-23235993)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30776138-30781137)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34167438-34172437)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63217594-63222593)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51286044-51291043)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35500989-35505988)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36433441-36438440)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48706372-48711371)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20393428-20398427)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7072056-7077055)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3781198-3786197)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51888917-51893916)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6761874-6766873)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13194144-13199143)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21366283-21371282)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74939193-74944192)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5593190-5598189)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100800043-100805042)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51499951-51504950)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33141446-33146445)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77739308-77744307)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26381239-26386238)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89800657-89805656)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 6082 generated ( 4.67846153846154 per locus)
Warning in plot_bw_profile(bwfiles = geo_CnR_bigwigs[4], bg_bwfiles = geo_CnR_bigwigs[3],  :
  Stderr estimate not available when normalizing by input

ggarrange(p1,p2,p3, ncol=3)

df1 <-  data.frame(set="top25_CTCF_G4", as.data.frame(bw_loci(bwfiles = geo_CnR_bigwigs[1:2],loci=top25.pds.CTCF_G4, labels=c("Mock","PDS")))[,6:7])
df2 <- data.frame(set="top25_CTCF_only", as.data.frame(bw_loci(bwfiles = geo_CnR_bigwigs[1:2],loci=top25.pds.CTCF_only, labels=c("Mock","PDS")))[,6:7])
df3 <- data.frame(set="bottom75", as.data.frame(bw_loci(bwfiles = geo_CnR_bigwigs[1:2],loci=bot75.pds, labels=c("Mock","PDS")))[,6:7])
df4 <- data.frame(set="Random", as.data.frame(bw_loci(bwfiles = geo_CnR_bigwigs[1:2], loci="../peaks/Control_peaks_shuffled.bed", labels=c("Mock","PDS")))[,6:7])

Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55179687-55180292)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59793658-59794279)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34556238-34556967)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2978464-2979272)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4607442-4607962)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156308831-156309336)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51511312-51511967)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52239000-52239584)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3555370-3556238)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180068925-180069824)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56797264-56798365)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1033502-1033933)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:364547-365162)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83222323-83222973)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46597450-46598598)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3472961-3473704)
Warning in .local(object, ...) :
  Failed to summarize range 162 (chr11:23220234-23221011)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1674595-1675345)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26034152-26034823)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85288833-85289387)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:671869-672525)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63139741-63140345)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2631786-2632455)
Warning in .local(object, ...) :
  Failed to summarize range 253 (chr3:6942745-6943305)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11579962-11580691)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27475365-27475821)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43354280-43354927)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14126157-14126925)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2018435-2019122)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71824474-71824879)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90691407-90691993)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85181983-85182565)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8740137-8740575)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28184600-28185097)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42220681-42221399)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61906246-61906960)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:701340-701770)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35282967-35283629)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21645364-21645811)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19787109-19787643)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1648211-1648602)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:638715-639243)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31207238-31207624)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:542549-542986)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112810767-112811414)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1582680-1583158)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67035356-67035921)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2253085-2253729)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:439965-440636)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1934585-1935212)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73696602-73697332)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38470010-38470557)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45580419-45581098)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19333243-19333698)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72045664-72046115)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2353039-2353658)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23628222-23628740)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35806633-35807087)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2253028-2254016)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15957606-15958038)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71736946-71737391)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46756573-46757158)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17281951-17282421)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79746101-79746686)
Warning in .local(object, ...) :
  Failed to summarize range 750 (chr18:3888059-3888386)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75428256-75428565)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2347318-2348098)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44770221-44770739)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13175516-13175846)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22300506-22300973)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4871827-4872226)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1978615-1979031)
Warning in .local(object, ...) :
  Failed to summarize range 819 (chr18:39600320-39601199)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71108134-71108607)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22337479-22338473)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32419424-32419821)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175746162-175746983)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:708156-708509)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170472177-170472598)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94980576-94981032)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67608501-67609162)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81111199-81111499)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5160142-5160515)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28472788-28473252)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11917922-11918659)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69234556-69235005)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3531327-3531987)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4155641-4156061)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:584950-585559)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75056404-75056940)
Warning in .local(object, ...) :
  Failed to summarize range 969 (chr6:5609454-5609961)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19019806-19020312)
Warning in .local(object, ...) :
  Failed to summarize range 986 (chr19:4063906-4064330)
Warning in .local(object, ...) :
  Failed to summarize range 994 (chr7:19033748-19034059)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72284341-72284957)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31206282-31206705)
Warning in .local(object, ...) :
  Failed to summarize range 1043 (chr2:16325688-16326424)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75455421-75456018)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23233329-23233660)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30778443-30778834)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34169678-34170199)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63219803-63220385)
Warning in .local(object, ...) :
  Failed to summarize range 1085 (chr2:27003216-27003648)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51288320-51288769)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35503302-35503677)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36435622-36436261)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48708502-48709243)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20395699-20396157)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7074252-7074861)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3783510-3783887)
Warning in .local(object, ...) :
  Failed to summarize range 1156 (chr2:95653606-95654120)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51891244-51891590)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6764158-6764590)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13196397-13196892)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21368577-21368990)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74941510-74941876)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5595447-5595934)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100802301-100802785)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51502322-51502580)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33143737-33144155)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77741413-77742204)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26383505-26383973)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89802910-89803405)
Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55179687-55180292)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59793658-59794279)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34556238-34556967)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2978464-2979272)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4607442-4607962)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156308831-156309336)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51511312-51511967)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52239000-52239584)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3555370-3556238)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180068925-180069824)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56797264-56798365)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1033502-1033933)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:364547-365162)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83222323-83222973)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46597450-46598598)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3472961-3473704)
Warning in .local(object, ...) :
  Failed to summarize range 162 (chr11:23220234-23221011)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1674595-1675345)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26034152-26034823)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85288833-85289387)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:671869-672525)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63139741-63140345)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2631786-2632455)
Warning in .local(object, ...) :
  Failed to summarize range 253 (chr3:6942745-6943305)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11579962-11580691)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27475365-27475821)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43354280-43354927)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14126157-14126925)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2018435-2019122)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71824474-71824879)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90691407-90691993)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85181983-85182565)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8740137-8740575)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28184600-28185097)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42220681-42221399)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61906246-61906960)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:701340-701770)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35282967-35283629)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21645364-21645811)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19787109-19787643)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1648211-1648602)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:638715-639243)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31207238-31207624)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:542549-542986)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112810767-112811414)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1582680-1583158)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67035356-67035921)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2253085-2253729)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:439965-440636)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1934585-1935212)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73696602-73697332)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38470010-38470557)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45580419-45581098)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19333243-19333698)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72045664-72046115)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2353039-2353658)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23628222-23628740)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35806633-35807087)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2253028-2254016)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15957606-15958038)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71736946-71737391)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46756573-46757158)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17281951-17282421)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79746101-79746686)
Warning in .local(object, ...) :
  Failed to summarize range 750 (chr18:3888059-3888386)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75428256-75428565)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2347318-2348098)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44770221-44770739)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13175516-13175846)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22300506-22300973)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4871827-4872226)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1978615-1979031)
Warning in .local(object, ...) :
  Failed to summarize range 819 (chr18:39600320-39601199)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71108134-71108607)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22337479-22338473)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32419424-32419821)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175746162-175746983)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:708156-708509)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170472177-170472598)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94980576-94981032)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67608501-67609162)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81111199-81111499)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5160142-5160515)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28472788-28473252)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11917922-11918659)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69234556-69235005)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3531327-3531987)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4155641-4156061)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:584950-585559)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75056404-75056940)
Warning in .local(object, ...) :
  Failed to summarize range 969 (chr6:5609454-5609961)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19019806-19020312)
Warning in .local(object, ...) :
  Failed to summarize range 986 (chr19:4063906-4064330)
Warning in .local(object, ...) :
  Failed to summarize range 994 (chr7:19033748-19034059)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72284341-72284957)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31206282-31206705)
Warning in .local(object, ...) :
  Failed to summarize range 1043 (chr2:16325688-16326424)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75455421-75456018)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23233329-23233660)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30778443-30778834)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34169678-34170199)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63219803-63220385)
Warning in .local(object, ...) :
  Failed to summarize range 1085 (chr2:27003216-27003648)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51288320-51288769)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35503302-35503677)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36435622-36436261)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48708502-48709243)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20395699-20396157)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7074252-7074861)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3783510-3783887)
Warning in .local(object, ...) :
  Failed to summarize range 1156 (chr2:95653606-95654120)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51891244-51891590)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6764158-6764590)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13196397-13196892)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21368577-21368990)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74941510-74941876)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5595447-5595934)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100802301-100802785)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51502322-51502580)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33143737-33144155)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77741413-77742204)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26383505-26383973)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89802910-89803405)

df <- rbind(df1,df2,df3,df4)
df$lfc.pds <- log2(df$PDS/df$Mock)
df$diff.pds <- df$PDS - df$Mock
mdf <- melt(df)

Warning in melt(df) :
  The melt generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(df). In the next version, this warning will become an error.
Using set as id variables

mdf$lg2 <- log2(mdf$value)

Warning: NaNs produced

ggviolin(mdf[mdf$variable %in% c("Mock","PDS"),], "set","lg2",fill="variable",palette = mypal, add="median_iqr")

Warning: Removed 16445 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 16445 rows containing non-finite outside the scale range (`stat_summary()`).

ggviolin(mdf[mdf$variable %in% "lfc.pds",], "set","value",fill="variable",palette = mypal, add="median_iqr") + geom_hline(yintercept = 0)

Warning: Removed 14181 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 14181 rows containing non-finite outside the scale range (`stat_summary()`).

ggviolin(mdf[mdf$variable %in% "diff.pds",], "set","value",fill="variable",palette = mypal, add="median_iqr") + coord_cartesian(ylim = c(-20,20)) + geom_hline(yintercept = 0)

Warning: Removed 123 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 123 rows containing non-finite outside the scale range (`stat_summary()`).

df1 <-  data.frame(set="top25_CTCF_G4", as.data.frame(bw_loci(bwfiles = geo_CnR_bigwigs[3:4],loci=top25.pdc.CTCF_G4, labels=c("Mock","PDC")))[,6:7])
df2 <- data.frame(set="top25_CTCF_only", as.data.frame(bw_loci(bwfiles = geo_CnR_bigwigs[3:4],loci=top25.pdc.CTCF_only, labels=c("Mock","PDC")))[,6:7])
df3 <- data.frame(set="bottom75", as.data.frame(bw_loci(bwfiles = geo_CnR_bigwigs[3:4],loci=bot75.pdc, labels=c("Mock","PDC")))[,6:7])
df4 <- data.frame(set="Random", as.data.frame(bw_loci(bwfiles = geo_CnR_bigwigs[3:4], loci="../peaks/Control_peaks_shuffled.bed", labels=c("Mock","PDC")))[,6:7])

Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55179687-55180292)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59793658-59794279)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34556238-34556967)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2978464-2979272)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4607442-4607962)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156308831-156309336)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51511312-51511967)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52239000-52239584)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3555370-3556238)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180068925-180069824)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56797264-56798365)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1033502-1033933)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:364547-365162)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83222323-83222973)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46597450-46598598)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3472961-3473704)
Warning in .local(object, ...) :
  Failed to summarize range 162 (chr11:23220234-23221011)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1674595-1675345)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26034152-26034823)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85288833-85289387)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:671869-672525)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63139741-63140345)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2631786-2632455)
Warning in .local(object, ...) :
  Failed to summarize range 253 (chr3:6942745-6943305)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11579962-11580691)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27475365-27475821)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43354280-43354927)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14126157-14126925)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2018435-2019122)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71824474-71824879)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90691407-90691993)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85181983-85182565)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8740137-8740575)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28184600-28185097)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42220681-42221399)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61906246-61906960)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:701340-701770)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35282967-35283629)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21645364-21645811)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19787109-19787643)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1648211-1648602)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:638715-639243)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31207238-31207624)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:542549-542986)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112810767-112811414)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1582680-1583158)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67035356-67035921)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2253085-2253729)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:439965-440636)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1934585-1935212)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73696602-73697332)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38470010-38470557)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45580419-45581098)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19333243-19333698)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72045664-72046115)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2353039-2353658)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23628222-23628740)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35806633-35807087)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2253028-2254016)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15957606-15958038)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71736946-71737391)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46756573-46757158)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17281951-17282421)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79746101-79746686)
Warning in .local(object, ...) :
  Failed to summarize range 750 (chr18:3888059-3888386)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75428256-75428565)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2347318-2348098)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44770221-44770739)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13175516-13175846)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22300506-22300973)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4871827-4872226)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1978615-1979031)
Warning in .local(object, ...) :
  Failed to summarize range 819 (chr18:39600320-39601199)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71108134-71108607)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22337479-22338473)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32419424-32419821)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175746162-175746983)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:708156-708509)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170472177-170472598)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94980576-94981032)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67608501-67609162)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81111199-81111499)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5160142-5160515)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28472788-28473252)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11917922-11918659)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69234556-69235005)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3531327-3531987)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4155641-4156061)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:584950-585559)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75056404-75056940)
Warning in .local(object, ...) :
  Failed to summarize range 969 (chr6:5609454-5609961)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19019806-19020312)
Warning in .local(object, ...) :
  Failed to summarize range 986 (chr19:4063906-4064330)
Warning in .local(object, ...) :
  Failed to summarize range 994 (chr7:19033748-19034059)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72284341-72284957)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31206282-31206705)
Warning in .local(object, ...) :
  Failed to summarize range 1043 (chr2:16325688-16326424)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75455421-75456018)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23233329-23233660)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30778443-30778834)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34169678-34170199)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63219803-63220385)
Warning in .local(object, ...) :
  Failed to summarize range 1085 (chr2:27003216-27003648)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51288320-51288769)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35503302-35503677)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36435622-36436261)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48708502-48709243)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20395699-20396157)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7074252-7074861)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3783510-3783887)
Warning in .local(object, ...) :
  Failed to summarize range 1156 (chr2:95653606-95654120)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51891244-51891590)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6764158-6764590)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13196397-13196892)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21368577-21368990)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74941510-74941876)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5595447-5595934)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100802301-100802785)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51502322-51502580)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33143737-33144155)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77741413-77742204)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26383505-26383973)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89802910-89803405)
Warning in .local(object, ...) :
  Failed to summarize range 3 (chr12:55179687-55180292)
Warning in .local(object, ...) :
  Failed to summarize range 15 (chrY:59793658-59794279)
Warning in .local(object, ...) :
  Failed to summarize range 20 (chrX:34556238-34556967)
Warning in .local(object, ...) :
  Failed to summarize range 39 (chr9:2978464-2979272)
Warning in .local(object, ...) :
  Failed to summarize range 49 (chr2:4607442-4607962)
Warning in .local(object, ...) :
  Failed to summarize range 53 (chr3:156308831-156309336)
Warning in .local(object, ...) :
  Failed to summarize range 58 (chrY:51511312-51511967)
Warning in .local(object, ...) :
  Failed to summarize range 67 (chrY:52239000-52239584)
Warning in .local(object, ...) :
  Failed to summarize range 87 (chrY:3555370-3556238)
Warning in .local(object, ...) :
  Failed to summarize range 90 (chr2:180068925-180069824)
Warning in .local(object, ...) :
  Failed to summarize range 106 (chrY:56797264-56798365)
Warning in .local(object, ...) :
  Failed to summarize range 108 (chr17:1033502-1033933)
Warning in .local(object, ...) :
  Failed to summarize range 124 (chr3:364547-365162)
Warning in .local(object, ...) :
  Failed to summarize range 127 (chrY:83222323-83222973)
Warning in .local(object, ...) :
  Failed to summarize range 137 (chrY:46597450-46598598)
Warning in .local(object, ...) :
  Failed to summarize range 159 (chr14:3472961-3473704)
Warning in .local(object, ...) :
  Failed to summarize range 162 (chr11:23220234-23221011)
Warning in .local(object, ...) :
  Failed to summarize range 166 (chr19:1674595-1675345)
Warning in .local(object, ...) :
  Failed to summarize range 195 (chr14:26034152-26034823)
Warning in .local(object, ...) :
  Failed to summarize range 197 (chr1:85288833-85289387)
Warning in .local(object, ...) :
  Failed to summarize range 208 (chr11:671869-672525)
Warning in .local(object, ...) :
  Failed to summarize range 210 (chr16:63139741-63140345)
Warning in .local(object, ...) :
  Failed to summarize range 233 (chr14:2631786-2632455)
Warning in .local(object, ...) :
  Failed to summarize range 253 (chr3:6942745-6943305)
Warning in .local(object, ...) :
  Failed to summarize range 258 (chrY:11579962-11580691)
Warning in .local(object, ...) :
  Failed to summarize range 264 (chrX:27475365-27475821)
Warning in .local(object, ...) :
  Failed to summarize range 270 (chrY:43354280-43354927)
Warning in .local(object, ...) :
  Failed to summarize range 272 (chrY:14126157-14126925)
Warning in .local(object, ...) :
  Failed to summarize range 298 (chr6:2018435-2019122)
Warning in .local(object, ...) :
  Failed to summarize range 306 (chr8:71824474-71824879)
Warning in .local(object, ...) :
  Failed to summarize range 349 (chr18:90691407-90691993)
Warning in .local(object, ...) :
  Failed to summarize range 376 (chr15:85181983-85182565)
Warning in .local(object, ...) :
  Failed to summarize range 406 (chrY:8740137-8740575)
Warning in .local(object, ...) :
  Failed to summarize range 427 (chrY:28184600-28185097)
Warning in .local(object, ...) :
  Failed to summarize range 430 (chr2:42220681-42221399)
Warning in .local(object, ...) :
  Failed to summarize range 432 (chrY:61906246-61906960)
Warning in .local(object, ...) :
  Failed to summarize range 466 (chr9:701340-701770)
Warning in .local(object, ...) :
  Failed to summarize range 470 (chrY:35282967-35283629)
Warning in .local(object, ...) :
  Failed to summarize range 471 (chr7:21645364-21645811)
Warning in .local(object, ...) :
  Failed to summarize range 474 (chr10:19787109-19787643)
Warning in .local(object, ...) :
  Failed to summarize range 480 (chr6:1648211-1648602)
Warning in .local(object, ...) :
  Failed to summarize range 500 (chr10:638715-639243)
Warning in .local(object, ...) :
  Failed to summarize range 502 (chrY:31207238-31207624)
Warning in .local(object, ...) :
  Failed to summarize range 508 (chr11:542549-542986)
Warning in .local(object, ...) :
  Failed to summarize range 511 (chr12:112810767-112811414)
Warning in .local(object, ...) :
  Failed to summarize range 525 (chr13:1582680-1583158)
Warning in .local(object, ...) :
  Failed to summarize range 531 (chrY:67035356-67035921)
Warning in .local(object, ...) :
  Failed to summarize range 535 (chr10:2253085-2253729)
Warning in .local(object, ...) :
  Failed to summarize range 544 (chr18:439965-440636)
Warning in .local(object, ...) :
  Failed to summarize range 546 (chr9:1934585-1935212)
Warning in .local(object, ...) :
  Failed to summarize range 565 (chrY:73696602-73697332)
Warning in .local(object, ...) :
  Failed to summarize range 569 (chr15:38470010-38470557)
Warning in .local(object, ...) :
  Failed to summarize range 592 (chr15:45580419-45581098)
Warning in .local(object, ...) :
  Failed to summarize range 623 (chrY:19333243-19333698)
Warning in .local(object, ...) :
  Failed to summarize range 640 (chrY:72045664-72046115)
Warning in .local(object, ...) :
  Failed to summarize range 646 (chr12:2353039-2353658)
Warning in .local(object, ...) :
  Failed to summarize range 653 (chr13:23628222-23628740)
Warning in .local(object, ...) :
  Failed to summarize range 658 (chr12:35806633-35807087)
Warning in .local(object, ...) :
  Failed to summarize range 659 (chr19:2253028-2254016)
Warning in .local(object, ...) :
  Failed to summarize range 701 (chrY:15957606-15958038)
Warning in .local(object, ...) :
  Failed to summarize range 706 (chrY:71736946-71737391)
Warning in .local(object, ...) :
  Failed to summarize range 722 (chrY:46756573-46757158)
Warning in .local(object, ...) :
  Failed to summarize range 732 (chr7:17281951-17282421)
Warning in .local(object, ...) :
  Failed to summarize range 744 (chr15:79746101-79746686)
Warning in .local(object, ...) :
  Failed to summarize range 750 (chr18:3888059-3888386)
Warning in .local(object, ...) :
  Failed to summarize range 759 (chr14:75428256-75428565)
Warning in .local(object, ...) :
  Failed to summarize range 761 (chr11:2347318-2348098)
Warning in .local(object, ...) :
  Failed to summarize range 767 (chr12:44770221-44770739)
Warning in .local(object, ...) :
  Failed to summarize range 772 (chrY:13175516-13175846)
Warning in .local(object, ...) :
  Failed to summarize range 780 (chrY:22300506-22300973)
Warning in .local(object, ...) :
  Failed to summarize range 783 (chr15:4871827-4872226)
Warning in .local(object, ...) :
  Failed to summarize range 806 (chr9:1978615-1979031)
Warning in .local(object, ...) :
  Failed to summarize range 819 (chr18:39600320-39601199)
Warning in .local(object, ...) :
  Failed to summarize range 850 (chr9:71108134-71108607)
Warning in .local(object, ...) :
  Failed to summarize range 851 (chr11:22337479-22338473)
Warning in .local(object, ...) :
  Failed to summarize range 858 (chrX:32419424-32419821)
Warning in .local(object, ...) :
  Failed to summarize range 869 (chr2:175746162-175746983)
Warning in .local(object, ...) :
  Failed to summarize range 871 (chr15:708156-708509)
Warning in .local(object, ...) :
  Failed to summarize range 880 (chrX:170472177-170472598)
Warning in .local(object, ...) :
  Failed to summarize range 899 (chr17:94980576-94981032)
Warning in .local(object, ...) :
  Failed to summarize range 906 (chr6:67608501-67609162)
Warning in .local(object, ...) :
  Failed to summarize range 909 (chrY:81111199-81111499)
Warning in .local(object, ...) :
  Failed to summarize range 922 (chrY:5160142-5160515)
Warning in .local(object, ...) :
  Failed to summarize range 926 (chrX:28472788-28473252)
Warning in .local(object, ...) :
  Failed to summarize range 928 (chrY:11917922-11918659)
Warning in .local(object, ...) :
  Failed to summarize range 930 (chrY:69234556-69235005)
Warning in .local(object, ...) :
  Failed to summarize range 938 (chr14:3531327-3531987)
Warning in .local(object, ...) :
  Failed to summarize range 954 (chr14:4155641-4156061)
Warning in .local(object, ...) :
  Failed to summarize range 955 (chr16:584950-585559)
Warning in .local(object, ...) :
  Failed to summarize range 961 (chr6:75056404-75056940)
Warning in .local(object, ...) :
  Failed to summarize range 969 (chr6:5609454-5609961)
Warning in .local(object, ...) :
  Failed to summarize range 983 (chrY:19019806-19020312)
Warning in .local(object, ...) :
  Failed to summarize range 986 (chr19:4063906-4064330)
Warning in .local(object, ...) :
  Failed to summarize range 994 (chr7:19033748-19034059)
Warning in .local(object, ...) :
  Failed to summarize range 999 (chrY:72284341-72284957)
Warning in .local(object, ...) :
  Failed to summarize range 1024 (chrY:31206282-31206705)
Warning in .local(object, ...) :
  Failed to summarize range 1043 (chr2:16325688-16326424)
Warning in .local(object, ...) :
  Failed to summarize range 1045 (chrY:75455421-75456018)
Warning in .local(object, ...) :
  Failed to summarize range 1059 (chrY:23233329-23233660)
Warning in .local(object, ...) :
  Failed to summarize range 1066 (chrX:30778443-30778834)
Warning in .local(object, ...) :
  Failed to summarize range 1067 (chrY:34169678-34170199)
Warning in .local(object, ...) :
  Failed to summarize range 1082 (chrY:63219803-63220385)
Warning in .local(object, ...) :
  Failed to summarize range 1085 (chr2:27003216-27003648)
Warning in .local(object, ...) :
  Failed to summarize range 1095 (chrY:51288320-51288769)
Warning in .local(object, ...) :
  Failed to summarize range 1102 (chrX:35503302-35503677)
Warning in .local(object, ...) :
  Failed to summarize range 1113 (chrY:36435622-36436261)
Warning in .local(object, ...) :
  Failed to summarize range 1115 (chr18:48708502-48709243)
Warning in .local(object, ...) :
  Failed to summarize range 1126 (chr8:20395699-20396157)
Warning in .local(object, ...) :
  Failed to summarize range 1127 (chr14:7074252-7074861)
Warning in .local(object, ...) :
  Failed to summarize range 1137 (chrY:3783510-3783887)
Warning in .local(object, ...) :
  Failed to summarize range 1156 (chr2:95653606-95654120)
Warning in .local(object, ...) :
  Failed to summarize range 1165 (chrY:51891244-51891590)
Warning in .local(object, ...) :
  Failed to summarize range 1178 (chr14:6764158-6764590)
Warning in .local(object, ...) :
  Failed to summarize range 1194 (chr17:13196397-13196892)
Warning in .local(object, ...) :
  Failed to summarize range 1195 (chr7:21368577-21368990)
Warning in .local(object, ...) :
  Failed to summarize range 1196 (chrY:74941510-74941876)
Warning in .local(object, ...) :
  Failed to summarize range 1199 (chr14:5595447-5595934)
Warning in .local(object, ...) :
  Failed to summarize range 1202 (chr12:100802301-100802785)
Warning in .local(object, ...) :
  Failed to summarize range 1203 (chr14:51502322-51502580)
Warning in .local(object, ...) :
  Failed to summarize range 1209 (chrX:33143737-33144155)
Warning in .local(object, ...) :
  Failed to summarize range 1217 (chrY:77741413-77742204)
Warning in .local(object, ...) :
  Failed to summarize range 1235 (chrY:26383505-26383973)
Warning in .local(object, ...) :
  Failed to summarize range 1259 (chrY:89802910-89803405)

df <- rbind(df1,df2,df3,df4)
df$lfc.pdc <- log2(df$PDC/df$Mock)
df$diff.pdc <- df$PDC - df$Mock
mdf <- melt(df)

Warning in melt(df) :
  The melt generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(df). In the next version, this warning will become an error.
Using set as id variables

mdf$lg2 <- log2(mdf$value)

Warning: NaNs produced

ggviolin(mdf[mdf$variable %in% c("Mock","PDC"),], "set","lg2",fill="variable",palette = mypal, add="median_iqr")

Warning: Removed 23839 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 23839 rows containing non-finite outside the scale range (`stat_summary()`).

ggviolin(mdf[mdf$variable %in% "lfc.pdc",], "set","value",fill="variable",palette = mypal, add="median_iqr") + geom_hline(yintercept = 0)

Warning: Removed 20154 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 20154 rows containing non-finite outside the scale range (`stat_summary()`).

ggviolin(mdf[mdf$variable %in% "diff.pdc",], "set","value",fill="variable",palette = mypal, add="median_iqr") + coord_cartesian(ylim = c(-20,20)) + geom_hline(yintercept = 0)

Warning: Removed 123 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 123 rows containing non-finite outside the scale range (`stat_summary()`).

top25.pds.CTCF_G4 <- makeGRangesFromDataFrame(results[(results$pds.quantile==4 & results$class == "CTCF_and_G4"),1:3],na.rm=T)
top25.pds.CTCF_only <- makeGRangesFromDataFrame(results[(results$pds.quantile==4  &  results$class == "CTCF_not_G4"),1:3],na.rm=T)

p1 <- plot_bw_profile(bwfiles = G4_bigwigs, loci = top25.pds.CTCF_G4, mode = "center",verbose = F, colors = mypal[3]) + coord_cartesian(ylim=c(0,10))
p2 <- plot_bw_profile(bwfiles = G4_bigwigs, loci = top25.pds.CTCF_only, mode = "center",verbose = F, colors = mypal[3]) + coord_cartesian(ylim=c(0,10))
ggarrange(p1,p2, ncol=2)

p1 <- plot_bw_profile(bwfiles = G4_bigwigs, loci = top25.pdc.CTCF_G4, mode = "center",verbose = F, colors = mypal[3]) + coord_cartesian(ylim=c(0,10))
p2 <- plot_bw_profile(bwfiles = G4_bigwigs, loci = top25.pdc.CTCF_only, mode = "center",verbose = F, colors = mypal[3]) + coord_cartesian(ylim=c(0,10))
ggarrange(p1,p2, ncol=2)

ord.top25 <- order(rowMeans(as.data.frame(bw_heatmap(bwfiles = geo_bigwigs[1],loci = top25.pds, mode = "center"))))
p1 <- plot_bw_heatmap(bwfiles = geo_bigwigs[1],loci = top25.pds, mode = "center",verbose = F, zmax = 10, max_rows_allowed = 50, order_by = ord.top25)
p2 <- plot_bw_heatmap(bwfiles = geo_bigwigs[2],loci = top25.pds, mode = "center",verbose = F, zmax = 10, max_rows_allowed = 50, order_by = ord.top25)
ggarrange(p1,p2, ncol=2, common.legend = T)
ggsave(glue("{plot_folder}Heatmap_CTCF_top25_PDSquantile.pdf"),
       plot = last_plot())

ord.bot75 <- order(rowMeans(as.data.frame(bw_heatmap(bwfiles = geo_bigwigs[1],loci = bot75.pds, mode = "center"))))
p1 <- plot_bw_heatmap(bwfiles = geo_bigwigs[1],loci = bot75.pds, mode = "center",verbose = F, zmax = 10, max_rows_allowed = 200, order_by = ord.bot75)
p2 <- plot_bw_heatmap(bwfiles = geo_bigwigs[2],loci = bot75.pds, mode = "center",verbose = F, zmax = 10, max_rows_allowed = 200, order_by = ord.bot75)
ggarrange(p1,p2, ncol=2, common.legend = T)
ggsave(glue("{plot_folder}Heatmap_CTCF_bot75_PDSquantile.pdf"),
       plot = last_plot())

G4_CnR <- bw_loci(c("../mendeley/FigureS2/GSM6634325_E14_Mock_G4.bw","../mendeley/FigureS2/GSM6634326_E14_PDS_G4.bw"),loci = makeGRangesFromDataFrame(results,na.rm=T),labels = c("Mock","PDS"))
results$G4_CnR_delta <- G4_CnR$PDS-G4_CnR$Mock
results$G4_CnR_lfc <- log2(G4_CnR$PDS/G4_CnR$Mock)
results$G4_CnR_mock <- G4_CnR$Mock

ggviolin(
  results,
  x = "pds.quantile",
  y = "G4_CnR_delta",
  fill = mypal[2],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-10, 15)) + geom_hline(yintercept = 1.55, linetype =
                                                    "dotted")
ggsave(glue("{plot_folder}Violin_G4_CnR_delta_by_PDSquantile.pdf"),
       plot = last_plot())

ggviolin(
  results,
  x = "pds.quantile",
  y = "G4_CnR_lfc",
  fill = mypal[2],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-10, 15)) + geom_hline(yintercept = 0, linetype =
                                                    "dotted")
ggsave(glue("{plot_folder}Violin_G4_CnR_delta_by_PDSquantile.pdf"),
       plot = last_plot())

compare_means(G4_CnR_lfc ~ pds.quantile, results)

results$pds.quartile.top25 <- results$pds.quantile == 4
mean(na.omit(results$G4_CnR_delta))
mean(results$G4_CnR_delta[results$pds.quartile.top25])
mean(results$G4_CnR_delta[!results$pds.quartile.top25])
compare_means(G4_CnR_delta ~ pds.quartile.top25, results)

export.bed(top25.pds,"../peaks/CTCF_peaks_top25_pds_up.bed")
export.bed(bot75.pds,"../peaks/CTCF_peaks_bot75_pds_up.bed")

Analysis by G4 motif

tr.G4 <- rtracklayer::import("../peaks/mm10_canonical_G4_PQS-regex.bed")  
tr.G4$name <- "G4"
top25.pds.G4anno <- bedscout::annotate_nearby_features(top25.pds,tr.G4,name_field = "name", distance_cutoff = 1000)
top25.pds.G4_1kb <- top25.pds.G4anno[!is.na(top25.pds.G4anno$nearby_features),]              
top25.pds.noG4 <- top25.pds.G4anno[is.na(top25.pds.G4anno$nearby_features),]               
                                
p1 <- plot_bw_profile(bwfiles = geo_bigwigs, loci = top25.pds.G4_1kb, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)

p2 <- plot_bw_profile(bwfiles = geo_bigwigs, loci = top25.pds.noG4, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)

ggarrange(p1,p2, ncol=2)

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[1:2],loci = top25.pds.G4_1kb, mode = "center",verbose = F, colors = mypal[c(1,2)]) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)

p2 <- plot_bw_profile(bwfiles = geo_bigwigs[1:2],loci = top25.pds.noG4, mode = "center",verbose = F, colors = mypal[c(1,2)]) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)

ggarrange(p1,p2, ncol=2)

ggsave(glue("{plot_folder}Profile_CTCF_top25_PDSquantile_byG4overlap.pdf"),
       plot = last_plot())

Saving 6 x 3 in image

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[2],bg_bwfiles = geo_bigwigs[1], loci = top25.pds.G4_1kb, mode = "center",verbose = F, colors = mypal[2],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in plot_bw_profile(bwfiles = geo_bigwigs[2], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

p2 <- plot_bw_profile(bwfiles = geo_bigwigs[2],bg_bwfiles = geo_bigwigs[1], loci = top25.pds.noG4, mode = "center",verbose = F, colors = mypal[2],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in plot_bw_profile(bwfiles = geo_bigwigs[2], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

ggarrange(p1,p2, ncol=2)

ggsave(glue("{plot_folder}Profile_CTCFfoldchange_top25_PDSquantile_byG4motif1kb.pdf"),
       plot = last_plot())

Saving 6 x 3 in image

top25.pdc.G4anno <- bedscout::annotate_nearby_features(top25.pdc,tr.G4,name_field = "name", distance_cutoff = 1000)
top25.pdc.G4_1kb <- top25.pds.G4anno[!is.na(top25.pds.G4anno$nearby_features),]              
top25.pdc.noG4 <- top25.pds.G4anno[is.na(top25.pds.G4anno$nearby_features),]               
                                
p1 <- plot_bw_profile(bwfiles = geo_bigwigs, loci = top25.pdc.G4_1kb, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)

p2 <- plot_bw_profile(bwfiles = geo_bigwigs, loci = top25.pdc.noG4, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)

ggarrange(p1,p2, ncol=2)

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[3],bg_bwfiles = geo_bigwigs[1], loci = top25.pdc.G4_1kb, mode = "center",verbose = F, colors = mypal[3],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in plot_bw_profile(bwfiles = geo_bigwigs[3], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

p2 <- plot_bw_profile(bwfiles = geo_bigwigs[3],bg_bwfiles = geo_bigwigs[1], loci = top25.pdc.noG4, mode = "center",verbose = F, colors = mypal[3],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in plot_bw_profile(bwfiles = geo_bigwigs[3], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

ggarrange(p1,p2, ncol=2)

ggsave(glue("{plot_folder}Profile_CTCFfoldchange_top25_PhenDC3quantile_byG4motif1kb.pdf"),
       plot = last_plot())

Saving 6 x 3 in image

tr.G4 <- rtracklayer::import("../peaks/mm10_canonical_G4_PQS-regex.bed")  
tr.G4$name <- "G4"
top25.pdc.G4anno <- bedscout::annotate_nearby_features(top25.pdc,tr.G4,name_field = "name", distance_cutoff = 1000)
top25.pdc.G4_1kb <- top25.pdc.G4anno[!is.na(top25.pdc.G4anno$nearby_features),]              
top25.pdc.noG4 <- top25.pdc.G4anno[is.na(top25.pdc.G4anno$nearby_features),]               
                                
p1 <- plot_bw_profile(bwfiles = geo_bigwigs, loci = top25.pdc.G4_1kb, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 260 generated ( 0.046594982078853 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 260 generated ( 0.046594982078853 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 260 generated ( 0.046594982078853 per locus)

p2 <- plot_bw_profile(bwfiles = geo_bigwigs, loci = top25.pdc.noG4, mode = "center",verbose = F, colors = mypal) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0442441622285948 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0442441622285948 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0442441622285948 per locus)

ggarrange(p1,p2, ncol=2)

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[c(1,3)],loci = top25.pdc.G4_1kb, mode = "center",verbose = F, colors = mypal[c(1,3)]) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 260 generated ( 0.046594982078853 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 260 generated ( 0.046594982078853 per locus)

p2 <- plot_bw_profile(bwfiles = geo_bigwigs[c(1,3)],loci = top25.pdc.noG4, mode = "center",verbose = F, colors = mypal[c(1,3)]) + coord_cartesian(ylim=c(0,10))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0442441622285948 per locus)
Warning in .summarize_matrix(fg, label) :
  Profile plot: 324 generated ( 0.0442441622285948 per locus)

ggarrange(p1,p2, ncol=2)

p1 <- plot_bw_profile(bwfiles = geo_bigwigs[3],bg_bwfiles = geo_bigwigs[1], loci = top25.pds.G4_1kb, mode = "center",verbose = F, colors = mypal[3],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 219 generated ( 0.0421884030052013 per locus)
Warning in plot_bw_profile(bwfiles = geo_bigwigs[3], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

p2 <- plot_bw_profile(bwfiles = geo_bigwigs[3],bg_bwfiles = geo_bigwigs[1], loci = top25.pds.noG4, mode = "center",verbose = F, colors = mypal[3],norm_mode = "log2fc",show_error = T) + coord_cartesian(ylim=c(-1,1))

Warning in .summarize_matrix(fg, label) :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in .summarize_matrix(bg, "bg") :
  Profile plot: 439 generated ( 0.0569242738589212 per locus)
Warning in plot_bw_profile(bwfiles = geo_bigwigs[3], bg_bwfiles = geo_bigwigs[1],  :
  Stderr estimate not available when normalizing by input

ggarrange(p1,p2, ncol=2)

Analysis by G4 quantile

ggviolin(
  results,
  x = "G4.quantile",
  y = "deseq.lfc.pds",
  fill = mypal[1],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-2, 2)) + geom_hline(yintercept = 0, linetype =
                                                    "dotted")
ggsave(glue("{plot_folder}Violin_CTCF_lfc_by_G4quantile.pdf"),
       plot = last_plot())

ggviolin(
  results,
  x = "G4.quantile",
  y = "log2.G4",
  fill = mypal2[5],
  add = "median_iqr"
) + geom_hline(yintercept = 0, linetype = "dotted")
ggsave(glue("{plot_folder}Violin_G4_by_G4quantile.pdf"), plot = last_plot())

peak_cats <- bedscout::import_named_bed_into_list(peaks_bed)
plot_bw_profile(
  G4_bigwigs,
  peak_cats,
  labels = c(
    peak_cats[[1]][1, ]$name,
    peak_cats[[2]][1, ]$name,
    peak_cats[[3]][1, ]$name,
    peak_cats[[4]][1, ]$name
  ),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal
)

plot_bw_profile(
  combined_bigwigs[1],
  peak_cats,
  labels = c(
    peak_cats[[1]][1, ]$name,
    peak_cats[[2]][1, ]$name,
    peak_cats[[3]][1, ]$name,
    peak_cats[[4]][1, ]$name
  ),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal
)

p1 <- plot_bw_profile(
  c(mocks_bigwigs, pds_bigwigs),
  peak_cats[[1]],
  labels = c("mock1", "mock2", "trt1", "rtr2"),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal2[c(9, 10, 5, 6)],
  upstream = 1500,
  downstream = 1500
)
p2 <- plot_bw_profile(
  c(mocks_bigwigs, pds_bigwigs),
  peak_cats[[2]],
  labels = c("mock1", "mock2", "trt1", "rtr2"),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal2[c(9, 10, 5, 6)],
  upstream = 1500,
  downstream = 1500
)
p3 <- plot_bw_profile(
  c(mocks_bigwigs, pds_bigwigs),
  peak_cats[[3]],
  labels = c("mock1", "mock2", "trt1", "rtr2"),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal2[c(9, 10, 5, 6)],
  upstream = 1500,
  downstream = 1500
)
p4 <- plot_bw_profile(
  c(mocks_bigwigs, pds_bigwigs),
  peak_cats[[4]],
  labels = c("mock1", "mock2", "trt1", "rtr2"),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal2[c(9, 10, 5, 6)],
  upstream = 1500,
  downstream = 1500
)

ggarrange(p1, p2, p3, p4, ncol = 4, nrow = 1)

p1 <- plot_bw_profile(
  c(mocks_bigwigs, pds_bigwigs),
  peak_cats[[1]],
  labels = c("mock1", "mock2", "trt1", "rtr2"),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal2[c(9, 10, 3, 4)],
  upstream = 1500,
  downstream = 1500
)
p2 <- plot_bw_profile(
  c(mocks_bigwigs, pds_bigwigs),
  peak_cats[[2]],
  labels = c("mock1", "mock2", "trt1", "rtr2"),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal2[c(9, 10, 3, 4)],
  upstream = 1500,
  downstream = 1500
)
p3 <- plot_bw_profile(
  c(mocks_bigwigs, pds_bigwigs),
  peak_cats[[3]],
  labels = c("mock1", "mock2", "trt1", "rtr2"),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal2[c(9, 10, 3, 4)],
  upstream = 1500,
  downstream = 1500
)
p4 <- plot_bw_profile(
  c(mocks_bigwigs, pds_bigwigs),
  peak_cats[[4]],
  labels = c("mock1", "mock2", "trt1", "rtr2"),
  mode = "center",
  show_error = T,
  verbose = F,
  remove_top = 0.001,
  colors = mypal2[c(9, 10, 3, 4)],
  upstream = 1500,
  downstream = 1500
)

ggarrange(p1, p2, p3, p4, ncol = 4, nrow = 1)

cen we learn something from the genes with top-most increase in CTCF?

sigup.pds <- results[results$deseq.sigup.pds, ]
sigup.pdc <- results[results$deseq.sigup.pdc, ]

#export.bed(sigup.pds,"peaks_sigup_pds.bed")
#export.bed(sigup.pds,"peaks_sigup_pds.bed")

gghistogram(results, "width", add = "median", fill = "class")

Distance-based analysis

G4_bed <- import('../data/G4_CnT/G4_WT_peaks.narrowPeak')
ATAC_bed <- import('../data/ATAC-seq/ATAC_seq_mESC_Martire_peaks.narrowPeak')
pro_bed <- import('../data/regions/promoters_geneSymbol.mm10.bed')

G4_bed <- bedscout::annotate_overlapping_features(G4_bed, pro_bed, name_field = "name")

G4_bed$name <- "G4"
G4_bed$name[!is.na(G4_bed$nearby_features)] <- "G4pro"
G4_bed$name[grepl("pro", G4_bed$name)] <- "G4pro"

nearest_G4_1kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4_bed,
  distance_cutoff = 1000,
  ignore.strand = T,
  name_field = "name"
)
nearest_G4_2.5kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4_bed,
  distance_cutoff = 2500,
  ignore.strand = T,
  name_field = "name"
)
nearest_G4_5kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4_bed,
  distance_cutoff = 5000,
  ignore.strand = T,
  name_field = "name"
)
nearest_G4_10kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4_bed,
  distance_cutoff = 10000,
  ignore.strand = T,
  name_field = "name"
)
nearest_G4_50kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4_bed,
  distance_cutoff = 50000,
  ignore.strand = T,
  name_field = "name"
)

ctcf$nearest_G4 <- factor(">50kb",
                          levels = c("<1kb", "<2.5kb", "<5kb", "<10kb", "<50kb", ">50kb"))
ctcf$nearest_G4[!is.na(nearest_G4_50kb$nearby_features)] <- "<50kb"
ctcf$nearest_G4[!is.na(nearest_G4_10kb$nearby_features)] <- "<10kb"
ctcf$nearest_G4[!is.na(nearest_G4_5kb$nearby_features)] <- "<5kb"
ctcf$nearest_G4[!is.na(nearest_G4_2.5kb$nearby_features)] <- "<2.5kb"
ctcf$nearest_G4[!is.na(nearest_G4_1kb$nearby_features)] <- "<1kb"

ctcf$nearest_G4_type <- "none"
ctcf$nearest_G4_type[!is.na(nearest_G4_50kb$nearby_features)] <- nearest_G4_50kb$nearby_features[!is.na(nearest_G4_50kb$nearby_features)]
ctcf$nearest_G4_type[!is.na(nearest_G4_10kb$nearby_features)] <- nearest_G4_10kb$nearby_features[!is.na(nearest_G4_10kb$nearby_features)]
ctcf$nearest_G4_type[!is.na(nearest_G4_5kb$nearby_features)] <- nearest_G4_5kb$nearby_features[!is.na(nearest_G4_5kb$nearby_features)]
ctcf$nearest_G4_type[!is.na(nearest_G4_2.5kb$nearby_features)] <- nearest_G4_2.5kb$nearby_features[!is.na(nearest_G4_2.5kb$nearby_features)]
ctcf$nearest_G4_type[!is.na(nearest_G4_1kb$nearby_features)] <- nearest_G4_1kb$nearby_features[!is.na(nearest_G4_1kb$nearby_features)]

ctcf$nearest_G4_type[grep("pro", ctcf$nearest_G4_type)] <- "G4pro"

results$nearest_G4 <- ctcf$nearest_G4
results$nearest_G4_type <- ctcf$nearest_G4_type
table(results$nearest_G4)
table(results$nearest_G4_type)
table(results$nearest_G4, results$nearest_G4_type)

ggviolin(
  results,
  x = "nearest_G4",
  y = "mean.mock",
  fill = mypal[1],
  add = "median_iqr"
) + coord_cartesian(ylim = c(0, 10)) +
  stat_compare_means(label.y = 8,
                     label.x = 3,
                     size = 3) +
  geom_hline(yintercept = 0, linetype = "dotted")
ggsave(glue("{plot_folder}Violin_CTCF_signal_by_G4distance.pdf"),
       plot = last_plot())

ggviolin(
  results,
  x = "nearest_G4",
  y = "deseq.lfc.pds",
  fill = mypal[1],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-4, 4)) + geom_hline(yintercept = 0, linewidth = 0.2) +
  geom_hline(
    yintercept = median(results$deseq.lfc.pds[results$nearest_G4 == "<1kb"]),
    linetype = "dotted",
    linewidth = 0.2
  ) +
  stat_compare_means(label.y = 3,
                     label.x = 2,
                     size = 3)
ggsave(glue("{plot_folder}Violin_CTCF_PDS_lfc_by_G4distance.pdf"),
       plot = last_plot())

nearest_G4_stats = compare_means(deseq.lfc.pds ~ nearest_G4, results)
nearest_G4_stats
write_tsv(nearest_G4_stats,
          glue("{stat_output}pds_G4distance_plots-statistics.tsv"))

ggviolin(
  results,
  x = "nearest_G4",
  y = "deseq.lfc.pdc",
  fill = mypal[1],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-2, 2)) + geom_hline(yintercept = 0, linewidth = 0.2) + geom_hline(
  yintercept = mean(results$deseq.lfc.pdc[results$nearest_G4 == "<1kb"]),
  linetype = "dotted",
  linewidth = 0.2
)
ggsave(glue("{plot_folder}Violin_CTCF_PhenDC3_lfc_by_G4distance.pdf"), plot = last_plot())

nearest_G4_stats = compare_means(deseq.lfc.pdc ~ nearest_G4, results)
nearest_G4_stats
write_tsv(nearest_G4_stats, glue("{stat_output}phendc_G4distance_plots-statistics.tsv"))

ggviolin(
  results,
  x = "nearest_G4",
  y = "deseq.lfc.pds",
  fill = "nearest_G4_type",
  palette = mypal[c(1, 3, 5)],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-2, 4)) + geom_hline(yintercept = 0, linewidth = 0.2) + geom_hline(
  yintercept = mean(results$deseq.lfc.pds[results$nearest_G4 == "<1kb"]),
  linetype = "dotted",
  linewidth = 0.2
) +
  stat_compare_means(aes(group = nearest_G4_type))
ggsave(glue("{plot_folder}Violin_CTCF_PDS_lfc_by_G4distance_pro.pdf"),
       plot = last_plot())

compare_means(deseq.lfc.pds ~ nearest_G4, results[results$nearest_G4_type ==
                                                    "G4", ])
compare_means(deseq.lfc.pds ~ nearest_G4, results[results$nearest_G4_type ==
                                                    "G4", ]) %>%
  write_tsv(.,
            glue(
              "{stat_output}pds_G4distance_plots-nearest_G4-statistics.tsv"
            ))

compare_means(deseq.lfc.pds ~ nearest_G4, results[results$nearest_G4_type ==
                                                    "G4pro", ])
compare_means(deseq.lfc.pds ~ nearest_G4, results[results$nearest_G4_type ==
                                                    "G4pro", ]) %>%
  write_tsv(.,
            glue(
              "{stat_output}pds_G4distance_plots-nearest_G4pro-statistics.tsv"
            ))

ggviolin(
  results,
  x = "nearest_G4",
  y = "deseq.lfc.pdc",
  fill = "nearest_G4_type",
  palette = mypal[c(1, 3, 5)],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-2, 2)) + geom_hline(yintercept = 0, linewidth = 0.2) + geom_hline(
  yintercept = mean(results$deseq.lfc.pdc[results$nearest_G4 == "<1kb"]),
  linetype = "dotted",
  linewidth = 0.2
)
ggsave(glue(
  "{plot_folder}Violin_CTCF_PhenDC3_lfc_by_G4distance_pro.pdf"
),
plot = last_plot())

compare_means(deseq.lfc.pdc ~ nearest_G4, results[results$nearest_G4_type ==
                                                    "G4", ])
compare_means(deseq.lfc.pdc ~ nearest_G4, results[results$nearest_G4_type ==
                                                    "G4", ]) %>%
  write_tsv(.,
            glue(
              "{stat_output}phendc_G4distance_plots-nearest_G4-statistics.tsv"
            ))

compare_means(deseq.lfc.pdc ~ nearest_G4, results[results$nearest_G4_type ==
                                                    "G4pro", ])
compare_means(deseq.lfc.pdc ~ nearest_G4, results[results$nearest_G4_type ==
                                                    "G4pro", ]) %>%
  write_tsv(.,
            glue(
              "{stat_output}phendc_G4distance_plots-nearest_G4pro-statistics.tsv"
            ))

Distance-based analysis, this time with predicted G4 motifs, not experimental peaks

#results <- read.table(glue("{result_folder}foldchange_results.txt"))
results$class <- factor(results$class, levels = c("CTCF_and_G4", "CTCF_not_G4"))
G4_bed <- import('../data/G4_CnT/G4_WT_peaks.narrowPeak')
G4_bed$name <- "peak"
G4pred_bed <- import('../data/predG4/mm10_canonical_G4_PQS-regex.bed')
ATAC_bed <- import('../data/ATAC-seq/ATAC_seq_mESC_Martire_peaks.narrowPeak')
pro_bed <- import('../data/regions/promoters_geneSymbol.mm10.bed')

G4pred_bed <- bedscout::annotate_overlapping_features(G4pred_bed, G4_bed, name_field = "name")

G4pred_bed$name <- "G4pred"
G4pred_bed$name[grepl("peak", G4pred_bed$nearby_features)] <- "G4exp"

table(G4pred_bed$name)

nearest_G4_0kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4pred_bed,
  distance_cutoff = 0,
  ignore.strand = T,
  name_field = "name"
)
nearest_G4_1kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4pred_bed,
  distance_cutoff = 1000,
  ignore.strand = T,
  name_field = "name"
)
nearest_G4_2.5kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4pred_bed,
  distance_cutoff = 2500,
  ignore.strand = T,
  name_field = "name"
)
nearest_G4_5kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4pred_bed,
  distance_cutoff = 5000,
  ignore.strand = T,
  name_field = "name"
)
nearest_G4_10kb <- bedscout::annotate_nearby_features(
  ctcf,
  G4pred_bed,
  distance_cutoff = 10000,
  ignore.strand = T,
  name_field = "name"
)


ctcf$nearest_G4 <- factor(">10kb",
                          levels = c("0kb", "<1kb", "<2.5kb", "<5kb", "<10kb", ">10kb"))
ctcf$nearest_G4[!is.na(nearest_G4_10kb$nearby_features)] <- "<10kb"
ctcf$nearest_G4[!is.na(nearest_G4_5kb$nearby_features)] <- "<5kb"
ctcf$nearest_G4[!is.na(nearest_G4_2.5kb$nearby_features)] <- "<2.5kb"
ctcf$nearest_G4[!is.na(nearest_G4_1kb$nearby_features)] <- "<1kb"
ctcf$nearest_G4[!is.na(nearest_G4_0kb$nearby_features)] <- "0kb"

results$nearest_G4 <- ctcf$nearest_G4
table(results$nearest_G4)
table(results$nearest_G4, results$pro)

mdf <- reshape2::melt(table(results$nearest_G4, results$pro))
ggplot(mdf, aes(Var1, Var2, fill = value)) +
  geom_tile(show.legend = F) + geom_text(aes(label = value)) +
  scale_fill_gradient(low = "white", high = "orange") + theme_minimal()
ggsave(glue("{plot_folder}Heatmap_CTCF_sites_by_predG4distance.pdf"),
       plot = last_plot())

ggviolin(
  results,
  x = "nearest_G4",
  y = "mean.mock",
  fill = mypal[1],
  add = "median_iqr"
) + coord_cartesian(ylim = c(0, 10)) + geom_hline(yintercept = 0, linetype =
                                                    "dotted") +
  stat_compare_means(
    aes(group = nearest_G4),
    label.y = 8,
    label.x = 2,
    size = 3
  )
ggsave(glue(
  "{plot_folder}Violin_CTCF_signal_by_predG4distance.pdf"),
  plot = last_plot())

ggviolin(
  results,
  x = "nearest_G4",
  y = "deseq.lfc.pds",
  fill = mypal[1],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-0.5, 1.5)) + geom_hline(yintercept = 0, linewidth = 0.2) + geom_hline(
  yintercept = median(results$deseq.lfc.pds[results$nearest_G4 == "0kb"]),
  linetype = "dotted",
  linewidth = 0.2
) +
  stat_compare_means(label.y = 1.3,
                     label.x = 3,
                     size = 2)
ggsave(glue("{plot_folder}Violin_CTCF_PDS_lfc_by_predG4distance.pdf"),
       plot = last_plot())

compare_means(deseq.lfc.pds ~ nearest_G4, results)

ggviolin(
  results,
  x = "nearest_G4",
  y = "deseq.lfc.pdc",
  fill = mypal[1],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-0.5, 1.5)) + geom_hline(yintercept = 0, linewidth = 0.2) + geom_hline(
  yintercept = mean(results$deseq.lfc.pdc[results$nearest_G4 == "0kb"]),
  linetype = "dotted",
  linewidth = 0.2
) +
  stat_compare_means(label.y = 1.3,
                     label.x = 3,
                     size = 2)
ggsave(glue(
  "{plot_folder}Violin_CTCF_PhenDC3_lfc_by_predG4distance.pdf"
),
plot = last_plot())

compare_means(deseq.lfc.pdc ~ nearest_G4, results)

ggviolin(
  results,
  x = "nearest_G4",
  y = "deseq.lfc.pds",
  fill = "pro",
  palette = mypal[c(1, 3, 5)],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-0.5, 1.5)) + geom_hline(yintercept = 0, linewidth = 0.2) + geom_hline(
  yintercept = mean(results$deseq.lfc.pds[results$nearest_G4 == "0kb"]),
  linetype = "dotted",
  linewidth = 0.2
) +
  stat_compare_means(aes(group = pro),
                     label.y = 1.3,
                     label.x = 3,
                     size = 1.5)
ggsave(glue("{plot_folder}Violin_CTCF_PDS_lfc_by_predG4distance_pro.pdf"), plot = last_plot())

```{ r } compare_means(deseq.lfc.pds ~ nearest_G4, results[results\(pro == "noPro", ]) compare_means(deseq.lfc.pds ~ nearest_G4, results[results\)pro == “noPro”, ]) %>% write_tsv(., “pds_G4distance_plots-noPro-statistics.tsv”)

<!-- rnb-text-end -->


<!-- rnb-chunk-begin -->


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```r
compare_means(deseq.lfc.pds ~ nearest_G4, results[results$pro == "Pro", ]) %>%
  write_tsv(.,
            glue("{stat_output}pds_G4distance_plots-Pro-statistics.tsv"))

compare_means(deseq.lfc.pds ~ pro, group.by = "nearest_G4", results) %>%
  write_tsv(.,
            glue(
              "{stat_output}pds_G4distance_plots-between_prom_types_stats.tsv"
            ))

compare_means(deseq.lfc.pds ~ nearest_G4, group.by = "pro", results) %>%
  write_tsv(.,
            glue(
              "{stat_output}pds_G4distance_plots-within_prom_types_stats.tsv"
            ))

ggviolin(
  results,
  x = "nearest_G4",
  y = "deseq.lfc.pdc",
  fill = "pro",
  palette = mypal[c(1, 3, 5)],
  add = "median_iqr"
) + coord_cartesian(ylim = c(-0.5, 1.5)) + geom_hline(yintercept = 0, linewidth = 0.2) + geom_hline(
  yintercept = mean(results$deseq.lfc.pdc[results$nearest_G4 == "0kb"]),
  linetype = "dotted",
  linewidth = 0.2
) +
  stat_compare_means(aes(group = pro),
                     label.y = 1.3,
                     label.x = 3,
                     size = 1.5)
ggsave(glue(
  "{plot_folder}Violin_CTCF_PhenDC3_lfc_by_predG4distance_pro.pdf"
),
plot = last_plot())

compare_means(deseq.lfc.pdc ~ nearest_G4, results[results$pro == "noPro", ]) %>%
  write_tsv(.,
            glue(
              "{stat_output}phendc_G4distance_plots-noPro-statistics.tsv"
            ))

compare_means(deseq.lfc.pdc ~ pro, group.by = "nearest_G4", results) %>%
  write_tsv(.,
            glue(
              "{stat_output}phendc_G4distance_plots-between_prom_types_stats.tsv"
            ))

compare_means(deseq.lfc.pdc ~ nearest_G4, group.by = "pro", results) %>%
  write_tsv(.,
            glue(
              "{stat_output}phendc_G4distance_plots-within_prom_types_stats.tsv"
            ))